diff --git a/packages/babel-cli/src/_babel-node.js b/packages/babel-cli/src/_babel-node.js
index ee6e340c31..28b62dd2c0 100644
--- a/packages/babel-cli/src/_babel-node.js
+++ b/packages/babel-cli/src/_babel-node.js
@@ -3,7 +3,6 @@ import Module from "module";
 import { inspect } from "util";
 import path from "path";
 import repl from "repl";
-import { util } from "babel-core";
 import * as babel from "babel-core";
 import vm from "vm";
 import "babel-polyfill";
@@ -13,13 +12,24 @@ import pkg from "../package.json";
 
 const program = new commander.Command("babel-node");
 
+function collect(value, previousValue): Array<string> {
+  // If the user passed the option with no value, like "babel-node file.js --presets", do nothing.
+  if (typeof value !== "string") return previousValue;
+
+  const values = value.split(",");
+
+  return previousValue ? previousValue.concat(values) : values;
+}
+
+/* eslint-disable max-len */
 program.option("-e, --eval [script]", "Evaluate script");
 program.option("-p, --print [code]", "Evaluate script and print result");
-program.option("-o, --only [globs]", "");
-program.option("-i, --ignore [globs]", "");
-program.option("-x, --extensions [extensions]", "List of extensions to hook into [.es6,.js,.es,.jsx]");
-program.option("-w, --plugins [string]", "", util.list);
-program.option("-b, --presets [string]", "", util.list);
+program.option("-o, --only [globs]", "A comma-separated list of glob patterns to compile", collect);
+program.option("-i, --ignore [globs]", "A comma-separated list of glob patterns to skip compiling", collect);
+program.option("-x, --extensions [extensions]", "List of extensions to hook into [.es6,.js,.es,.jsx]", collect);
+program.option("-w, --plugins [string]", "", collect);
+program.option("-b, --presets [string]", "", collect);
+/* eslint-enable max-len */
 
 program.version(pkg.version);
 program.usage("[options] [ -e script | script.js ] [arguments]");
diff --git a/packages/babel-cli/src/babel-external-helpers.js b/packages/babel-cli/src/babel-external-helpers.js
index 76552a3a71..6624b64d65 100755
--- a/packages/babel-cli/src/babel-external-helpers.js
+++ b/packages/babel-cli/src/babel-external-helpers.js
@@ -1,7 +1,16 @@
 import commander from "commander";
-import { util, buildExternalHelpers } from "babel-core";
+import { buildExternalHelpers } from "babel-core";
 
-commander.option("-l, --whitelist [whitelist]", "Whitelist of helpers to ONLY include", util.list);
+function collect(value, previousValue): Array<string> {
+  // If the user passed the option with no value, like "babel-external-helpers --whitelist", do nothing.
+  if (typeof value !== "string") return previousValue;
+
+  const values = value.split(",");
+
+  return previousValue ? previousValue.concat(values) : values;
+}
+
+commander.option("-l, --whitelist [whitelist]", "Whitelist of helpers to ONLY include", collect);
 commander.option("-t, --output-type [type]", "Type of output (global|umd|var)", "global");
 
 commander.usage("[options]");
diff --git a/packages/babel-cli/src/babel/dir.js b/packages/babel-cli/src/babel/dir.js
index 7a19148bd7..1113fd9afc 100644
--- a/packages/babel-cli/src/babel/dir.js
+++ b/packages/babel-cli/src/babel/dir.js
@@ -8,6 +8,8 @@ import * as util from "./util";
 
 export default function (commander, filenames, opts) {
   function write(src, relative) {
+    if (!util.isCompilableExtension(relative, commander.extensions)) return false;
+
     // remove extension and then append back on .js
     relative = relative.replace(/\.(\w*?)$/, "") + ".js";
 
@@ -17,7 +19,8 @@ export default function (commander, filenames, opts) {
       sourceFileName: slash(path.relative(dest + "/..", src)),
       sourceMapTarget: path.basename(relative),
     }, opts));
-    if (!commander.copyFiles && data.ignored) return;
+
+    if (!data) return false;
 
     // we've requested explicit sourcemaps to be written to disk
     if (data.map && commander.sourceMaps && commander.sourceMaps !== "inline") {
@@ -30,14 +33,14 @@ export default function (commander, filenames, opts) {
     util.chmod(src, dest);
 
     util.log(src + " -> " + dest);
+
+    return true;
   }
 
   function handleFile(src, filename) {
-    if (util.shouldIgnore(src, opts)) return;
+    const didWrite = write(src, filename);
 
-    if (util.canCompile(filename, commander.extensions)) {
-      write(src, filename);
-    } else if (commander.copyFiles) {
+    if (!didWrite && commander.copyFiles) {
       const dest = path.join(commander.outDir, filename);
       outputFileSync(dest, fs.readFileSync(src));
       util.chmod(src, dest);
diff --git a/packages/babel-cli/src/babel/file.js b/packages/babel-cli/src/babel/file.js
index 181432c1e6..689f8f9353 100644
--- a/packages/babel-cli/src/babel/file.js
+++ b/packages/babel-cli/src/babel/file.js
@@ -124,8 +124,6 @@ export default function (commander, filenames, opts) {
     });
 
     _filenames.forEach(function (filename) {
-      if (util.shouldIgnore(filename, opts)) return;
-
       let sourceFilename = filename;
       if (commander.outFile) {
         sourceFilename = path.relative(path.dirname(commander.outFile), sourceFilename);
@@ -136,7 +134,8 @@ export default function (commander, filenames, opts) {
         sourceFileName: sourceFilename,
       }, opts));
 
-      if (data.ignored) return;
+      if (!data) return;
+
       results.push(data);
     });
 
@@ -159,7 +158,7 @@ export default function (commander, filenames, opts) {
           pollInterval: 10,
         },
       }).on("all", function (type, filename) {
-        if (util.shouldIgnore(filename, opts) || !util.canCompile(filename, commander.extensions)) return;
+        if (!util.isCompilableExtension(filename, commander.extensions)) return;
 
         if (type === "add" || type === "change") {
           util.log(type + " " + filename);
diff --git a/packages/babel-cli/src/babel/index.js b/packages/babel-cli/src/babel/index.js
index 99da42c6df..732ba1b011 100755
--- a/packages/babel-cli/src/babel/index.js
+++ b/packages/babel-cli/src/babel/index.js
@@ -2,7 +2,7 @@
 
 import fs from "fs";
 import commander from "commander";
-import { util, version } from "babel-core";
+import { version } from "babel-core";
 import uniq from "lodash/uniq";
 import glob from "glob";
 
@@ -11,17 +11,38 @@ import fileCommand from "./file";
 
 import pkg from "../../package.json";
 
+function booleanify(val: any): boolean | any {
+  if (val === "true" || val == 1) {
+    return true;
+  }
+
+  if (val === "false" || val == 0 || !val) {
+    return false;
+  }
+
+  return val;
+}
+
+function collect(value, previousValue): Array<string> {
+  // If the user passed the option with no value, like "babel file.js --presets", do nothing.
+  if (typeof value !== "string") return previousValue;
+
+  const values = value.split(",");
+
+  return previousValue ? previousValue.concat(values) : values;
+}
+
 /* eslint-disable max-len */
 // Standard Babel input configs.
 commander.option("-f, --filename [filename]", "filename to use when reading from stdin - this will be used in source-maps, errors etc");
-commander.option("--presets [list]", "comma-separated list of preset names");
-commander.option("--plugins [list]", "comma-separated list of plugin names");
+commander.option("--presets [list]", "comma-separated list of preset names", collect);
+commander.option("--plugins [list]", "comma-separated list of plugin names", collect);
 
 // Basic file input configuration.
 commander.option("--source-type [script|module]", "");
 commander.option("--no-babelrc", "Whether or not to look up .babelrc and .babelignore files");
-commander.option("--ignore [list]", "list of glob paths to **not** compile");
-commander.option("--only [list]", "list of glob paths to **only** compile");
+commander.option("--ignore [list]", "list of glob paths to **not** compile", collect);
+commander.option("--only [list]", "list of glob paths to **only** compile", collect);
 
 // Misc babel config.
 commander.option("--no-highlight-code", "enable/disable ANSI syntax highlighting of code frames (on by default)");
@@ -29,13 +50,13 @@ commander.option("--no-highlight-code", "enable/disable ANSI syntax highlighting
 // General output formatting.
 commander.option("--no-comments", "write comments to generated output (true by default)");
 commander.option("--retain-lines", "retain line numbers - will result in really ugly code");
-commander.option("--compact [true|false|auto]", "do not include superfluous whitespace characters and line terminators");
+commander.option("--compact [true|false|auto]", "do not include superfluous whitespace characters and line terminators", booleanify);
 commander.option("--minified", "save as much bytes when printing [true|false]");
 commander.option("--auxiliary-comment-before [string]", "print a comment before any injected non-user code");
 commander.option("--auxiliary-comment-after [string]", "print a comment after any injected non-user code");
 
 // General soucemap formatting.
-commander.option("-s, --source-maps [true|false|inline|both]", "");
+commander.option("-s, --source-maps [true|false|inline|both]", "", booleanify);
 commander.option("--source-map-target [string]", "set `file` on returned source map");
 commander.option("--source-file-name [string]", "set `sources[0]` on returned source map");
 commander.option("--source-root [filename]", "the root from which all sources are relative");
@@ -46,7 +67,7 @@ commander.option("-M, --module-ids", "insert an explicit id for modules");
 commander.option("--module-id [string]", "specify a custom name for module ids");
 
 // "babel" command specific arguments that are not passed to babel-core.
-commander.option("-x, --extensions [extensions]", "List of extensions to compile when a directory has been input [.es6,.js,.es,.jsx]");
+commander.option("-x, --extensions [extensions]", "List of extensions to compile when a directory has been input [.es6,.js,.es,.jsx]", collect);
 commander.option("-w, --watch", "Recompile files on changes");
 commander.option("--skip-initial-build", "Do not compile files before watching");
 commander.option("-o, --out-file [out]", "Compile all input files into a single file");
@@ -61,12 +82,6 @@ commander.parse(process.argv);
 
 //
 
-if (commander.extensions) {
-  commander.extensions = util.arrayify(commander.extensions);
-}
-
-//
-
 const errors = [];
 
 let filenames = commander.args.reduce(function (globbed, input) {
@@ -130,16 +145,5 @@ if (opts.babelrc === true) opts.babelrc = undefined;
 if (opts.comments === true) opts.comments = undefined;
 if (opts.highlightCode === true) opts.highlightCode = undefined;
 
-opts.ignore = util.arrayify(opts.ignore, util.regexify);
-
-if (opts.only) {
-  opts.only = util.arrayify(opts.only, util.regexify);
-}
-
-if (opts.sourceMaps) opts.sourceMaps = util.booleanify(opts.sourceMaps);
-if (opts.compact) opts.compact = util.booleanify(opts.compact);
-if (opts.presets) opts.presets = util.list(opts.presets);
-if (opts.plugins) opts.plugins = util.list(opts.plugins);
-
 const fn = commander.outDir ? dirCommand : fileCommand;
 fn(commander, filenames, opts);
diff --git a/packages/babel-cli/src/babel/util.js b/packages/babel-cli/src/babel/util.js
index d95555ae1d..ef99088537 100644
--- a/packages/babel-cli/src/babel/util.js
+++ b/packages/babel-cli/src/babel/util.js
@@ -1,6 +1,7 @@
 import commander from "commander";
 import readdir from "fs-readdir-recursive";
 import * as babel from "babel-core";
+import includes from "lodash/includes";
 import path from "path";
 import fs from "fs";
 
@@ -10,16 +11,19 @@ export function chmod(src, dest) {
 
 export function readdirFilter(filename) {
   return readdir(filename).filter(function (filename) {
-    return babel.util.canCompile(filename);
+    return babel.util.isCompilableExtension(filename);
   });
 }
 
 export { readdir };
 
-export const canCompile = babel.util.canCompile;
-
-export function shouldIgnore(loc, opts) {
-  return babel.util.shouldIgnore(loc, opts.ignore, opts.only);
+/**
+ * Test if a filename ends with a compilable extension.
+ */
+export function isCompilableExtension(filename: string, altExts?: Array<string>): boolean {
+  const exts = altExts || babel.DEFAULT_EXTENSIONS;
+  const ext = path.extname(filename);
+  return includes(exts, ext);
 }
 
 export function addSourceMappingUrl(code, loc) {
@@ -35,16 +39,12 @@ export function transform(filename, code, opts) {
     filename,
   });
 
-  const result = babel.transform(code, opts);
-  result.filename = filename;
-  result.actual = code;
-  return result;
+  return babel.transform(code, opts);
 }
 
 export function compile(filename, opts) {
   try {
-    const code = fs.readFileSync(filename, "utf8");
-    return transform(filename, code, opts);
+    return babel.transformFileSync(filename, opts);
   } catch (err) {
     if (commander.watch) {
       console.error(toErrorStack(err));
diff --git a/packages/babel-cli/test/fixtures/babel/--ignore complete/options.json b/packages/babel-cli/test/fixtures/babel/--ignore complete/options.json
index c013d5d4da..b4c4db71f3 100644
--- a/packages/babel-cli/test/fixtures/babel/--ignore complete/options.json	
+++ b/packages/babel-cli/test/fixtures/babel/--ignore complete/options.json	
@@ -1,3 +1,3 @@
 {
-  "args": ["src", "--out-dir", "lib", "--ignore", "/bar/*"]
+  "args": ["src", "--out-dir", "lib", "--ignore", "src/bar"]
 }
diff --git a/packages/babel-cli/test/index.js b/packages/babel-cli/test/index.js
index c2bda15c4c..bb9746be70 100644
--- a/packages/babel-cli/test/index.js
+++ b/packages/babel-cli/test/index.js
@@ -91,7 +91,7 @@ const buildTest = function (binName, testName, opts) {
     }
 
     if (binName === "babel-node") {
-      args.push("--only", "packages/*/test");
+      args.push("--only", "../../../../packages/*/test");
     }
 
     args = args.concat(opts.args);
@@ -119,7 +119,7 @@ const buildTest = function (binName, testName, opts) {
       }
 
       if (err) {
-        err.message = args.join(" ") + ": " + err.message;
+        err.message = args.map((arg) => `"${ arg }"`).join(" ") + ": " + err.message;
       }
 
       callback(err);
diff --git a/packages/babel-core/package.json b/packages/babel-core/package.json
index 0c99b59385..2beae71fa0 100644
--- a/packages/babel-core/package.json
+++ b/packages/babel-core/package.json
@@ -39,7 +39,7 @@
     "debug": "^2.1.1",
     "json5": "^0.5.0",
     "lodash": "^4.2.0",
-    "minimatch": "^3.0.2",
+    "micromatch": "^2.3.11",
     "private": "^0.1.6",
     "resolve": "^1.3.2",
     "slash": "^1.0.0",
diff --git a/packages/babel-core/src/index.js b/packages/babel-core/src/index.js
index 164ccc21a9..f3fa340eb5 100644
--- a/packages/babel-core/src/index.js
+++ b/packages/babel-core/src/index.js
@@ -6,8 +6,6 @@ export resolvePreset from "./helpers/resolve-preset";
 export { version } from "../package";
 export { getEnv } from "./helpers/environment";
 
-export * as util from "./util";
-
 export * as messages from "babel-messages";
 export * as types from "babel-types";
 export traverse from "babel-traverse";
@@ -27,3 +25,8 @@ export {
   transformFileSync,
 } from "./transformation/pipeline";
 
+/**
+ * Recommended set of compilable extensions. Not used in babel-core directly, but meant as
+ * as an easy source for tooling making use of babel-core.
+ */
+export const DEFAULT_EXTENSIONS = Object.freeze([".js", ".jsx", ".es6", ".es"]);
diff --git a/packages/babel-core/src/transformation/file/index.js b/packages/babel-core/src/transformation/file/index.js
index 3eddf03235..9d5af49ff0 100644
--- a/packages/babel-core/src/transformation/file/index.js
+++ b/packages/babel-core/src/transformation/file/index.js
@@ -415,11 +415,7 @@ export default class File extends Store {
     code = code + "";
 
     try {
-      if (this.shouldIgnore()) {
-        return this.makeResult({ code, ignored: true });
-      } else {
-        return callback();
-      }
+      return callback();
     } catch (err) {
       if (err._babel) {
         throw err;
@@ -462,11 +458,6 @@ export default class File extends Store {
     this.addAst(ast);
   }
 
-  shouldIgnore() {
-    const opts = this.opts;
-    return util.shouldIgnore(opts.filename, opts.ignore, opts.only);
-  }
-
   call(key: "pre" | "post", pluginPasses: Array<PluginPass>) {
     for (const pass of pluginPasses) {
       const plugin = pass.plugin;
diff --git a/packages/babel-core/src/transformation/file/options/build-config-chain.js b/packages/babel-core/src/transformation/file/options/build-config-chain.js
index 11930db2cd..df05a06443 100644
--- a/packages/babel-core/src/transformation/file/options/build-config-chain.js
+++ b/packages/babel-core/src/transformation/file/options/build-config-chain.js
@@ -3,6 +3,7 @@ import resolve from "../../../helpers/resolve";
 import json5 from "json5";
 import path from "path";
 import fs from "fs";
+import micromatch from "micromatch";
 
 const existsCache = {};
 const jsonCache = {};
@@ -22,27 +23,104 @@ function exists(filename) {
 }
 
 export default function buildConfigChain(opts: Object = {}) {
-  const filename = opts.filename;
-  const builder = new ConfigChainBuilder();
+  const filename = opts.filename ? path.resolve(opts.filename) : null;
+  const builder = new ConfigChainBuilder(filename);
 
-  builder.mergeConfig({
-    options: opts,
-    alias: "base",
-    dirname: process.cwd(),
-  });
+  try {
+    builder.mergeConfig({
+      options: opts,
+      alias: "base",
+      dirname: process.cwd(),
+    });
 
-  // resolve all .babelrc files
-  if (opts.babelrc !== false) {
-    builder.findConfigs(filename);
+    // resolve all .babelrc files
+    if (opts.babelrc !== false) {
+      builder.findConfigs(filename);
+    }
+  } catch (e) {
+    if (e.code !== "BABEL_IGNORED_FILE") throw e;
+
+    return null;
   }
 
   return builder.configs.reverse();
 }
 
 class ConfigChainBuilder {
-  constructor() {
+  constructor(filename) {
     this.resolvedConfigs = [];
     this.configs = [];
+    this.filename = filename;
+    this.possibleDirs = null;
+  }
+
+  /**
+   * Tests if a filename should be ignored based on "ignore" and "only" options.
+   */
+  shouldIgnore(
+    ignore: Array<string | RegExp | Function>,
+    only?: Array<string | RegExp | Function>,
+    dirname: string,
+  ): boolean {
+    if (!this.filename) return false;
+
+    if (ignore) {
+      if (!Array.isArray(ignore)) {
+        throw new Error(`.ignore should be an array, was ${JSON.stringify(ignore)}`);
+      }
+
+      for (const pattern of ignore) {
+        if (this.matchesPattern(pattern, dirname)) return true;
+      }
+    }
+
+    if (only) {
+      if (!Array.isArray(only)) {
+        throw new Error(`.only should be an array, was ${JSON.stringify(only)}`);
+      }
+
+      for (const pattern of only) {
+        if (this.matchesPattern(pattern, dirname)) return false;
+      }
+      return true;
+    }
+
+    return false;
+  }
+
+  /**
+   * Returns result of calling function with filename if pattern is a function.
+   * Otherwise returns result of matching pattern Regex with filename.
+   */
+  matchesPattern(pattern: string | Function | RegExp, dirname: string) {
+    if (typeof pattern === "string") {
+      // Lazy-init so we don't initialize this for files that have no glob patterns.
+      if (!this.possibleDirs) {
+        this.possibleDirs = [];
+
+        if (this.filename) {
+          this.possibleDirs.push(this.filename);
+
+          let current = this.filename;
+          while (true) {
+            const previous = current;
+            current = path.dirname(current);
+            if (previous === current) break;
+
+            this.possibleDirs.push(current);
+          }
+        }
+      }
+
+      return this.possibleDirs.some(micromatch.filter(path.resolve(dirname, pattern), {
+        nocase: true,
+        nonegate: true,
+      }));
+    } else if (typeof pattern === "function") {
+      return pattern(this.filename);
+    } else {
+      return pattern.test(this.filename);
+    }
   }
 
   errorMultipleConfigs(loc1: string, loc2: string) {
@@ -171,6 +249,12 @@ class ConfigChainBuilder {
       return false;
     }
 
+    // Bail out ASAP if this file is ignored so that we run as little logic as possible on ignored files.
+    if (this.filename && this.shouldIgnore(options.ignore, options.only, dirname)) {
+      // TODO(logan): This is a really cross way to bail out. Avoid this in rewrite.
+      throw Object.assign(new Error("This file has been ignored."), { code: "BABEL_IGNORED_FILE" });
+    }
+
     options = Object.assign({}, options);
 
     loc = loc || alias;
diff --git a/packages/babel-core/src/transformation/file/options/option-manager.js b/packages/babel-core/src/transformation/file/options/option-manager.js
index 0eedbe8345..df43555c5f 100644
--- a/packages/babel-core/src/transformation/file/options/option-manager.js
+++ b/packages/babel-core/src/transformation/file/options/option-manager.js
@@ -236,17 +236,6 @@ export default class OptionManager {
       }
     }
 
-    if (opts.ignore) {
-      if (!Array.isArray(rawOpts.ignore)) throw new Error(`${alias}.ignore should be an array`);
-
-      opts.ignore = opts.ignore.map(util.regexify);
-    }
-    if (opts.only) {
-      if (!Array.isArray(rawOpts.only)) throw new Error(`${alias}.only should be an array`);
-
-      opts.only = opts.only.map(util.regexify);
-    }
-
     // resolve plugins
     if (opts.plugins) {
       if (!Array.isArray(rawOpts.plugins)) throw new Error(`${alias}.plugins should be an array`);
@@ -373,8 +362,11 @@ export default class OptionManager {
   }
 
   init(opts: Object = {}): Object {
+    const configChain = buildConfigChain(opts);
+    if (!configChain) return null;
+
     try {
-      for (const config of buildConfigChain(opts)) {
+      for (const config of configChain) {
         this.mergeOptions(config);
       }
     } catch (e) {
diff --git a/packages/babel-core/src/transformation/pipeline.js b/packages/babel-core/src/transformation/pipeline.js
index 367e1efede..9bf718a47e 100644
--- a/packages/babel-core/src/transformation/pipeline.js
+++ b/packages/babel-core/src/transformation/pipeline.js
@@ -17,6 +17,7 @@ export function analyse(code: string, opts: Object = {}, visitor?: Object): ?Bab
 
 export function transform(code: string, opts?: Object): BabelFileResult {
   opts = new OptionManager().init(opts);
+  if (opts === null) return null;
 
   const file = new File(opts);
   return file.wrap(code, function () {
@@ -28,6 +29,7 @@ export function transform(code: string, opts?: Object): BabelFileResult {
 
 export function transformFromAst(ast: Object, code: string, opts: Object): BabelFileResult {
   opts = new OptionManager().init(opts);
+  if (opts === null) return null;
 
   ast = normalizeAst(ast);
 
@@ -47,6 +49,7 @@ export function transformFile(filename: string, opts?: Object, callback: Functio
 
   opts.filename = filename;
   opts = new OptionManager().init(opts);
+  if (opts === null) return callback(null, null);
 
   fs.readFile(filename, function (err, code) {
     let result;
@@ -75,6 +78,7 @@ export function transformFile(filename: string, opts?: Object, callback: Functio
 export function transformFileSync(filename: string, opts?: Object = {}): string {
   opts.filename = filename;
   opts = new OptionManager().init(opts);
+  if (opts === null) return null;
 
   const code = fs.readFileSync(filename, "utf8");
   const file = new File(opts);
diff --git a/packages/babel-core/src/util.js b/packages/babel-core/src/util.js
index 51d42086c0..3caa4be75e 100644
--- a/packages/babel-core/src/util.js
+++ b/packages/babel-core/src/util.js
@@ -1,10 +1,3 @@
-import escapeRegExp from "lodash/escapeRegExp";
-import startsWith from "lodash/startsWith";
-import minimatch from "minimatch";
-import includes from "lodash/includes";
-import isRegExp from "lodash/isRegExp";
-import path from "path";
-import slash from "slash";
 import buildDebug from "debug";
 
 export { inherits, inspect } from "util";
@@ -22,140 +15,3 @@ export function message(opts: Object, msg: string) {
 
   return `[BABEL] ${opts.filename || "unknown"}: ${msg}`;
 }
-
-/**
- * Test if a filename ends with a compilable extension.
- */
-
-export function canCompile(filename: string, altExts?: Array<string>): boolean {
-  const exts = altExts || canCompile.EXTENSIONS;
-  const ext = path.extname(filename);
-  return includes(exts, ext);
-}
-
-/**
- * Default set of compilable extensions.
- */
-
-canCompile.EXTENSIONS = [".js", ".jsx", ".es6", ".es"];
-
-/**
- * Create an array from any value, splitting strings by ",".
- */
-
-export function list(val?: string): Array<string> {
-  if (!val) {
-    return [];
-  } else if (Array.isArray(val)) {
-    return val;
-  } else if (typeof val === "string") {
-    return val.split(",");
-  } else {
-    return [val];
-  }
-}
-
-/**
- * Create a RegExp from a string, array, or regexp.
- */
-
-export function regexify(val: any): RegExp {
-  if (!val) {
-    return new RegExp(/.^/);
-  }
-
-  if (Array.isArray(val)) {
-    val = new RegExp(val.map(escapeRegExp).join("|"), "i");
-  }
-
-  if (typeof val === "string") {
-    // normalise path separators
-    val = slash(val);
-
-    // remove starting wildcards or relative separator if present
-    if (startsWith(val, "./") || startsWith(val, "*/")) val = val.slice(2);
-    if (startsWith(val, "**/")) val = val.slice(3);
-
-    const regex = minimatch.makeRe(val, { nocase: true });
-    return new RegExp(regex.source.slice(1, -1), "i");
-  }
-
-  if (isRegExp(val)) {
-    return val;
-  }
-
-  throw new TypeError("illegal type for regexify");
-}
-
-/**
- * Create an array from a boolean, string, or array, mapped by and optional function.
- */
-
-export function arrayify(val: any, mapFn?: Function): Array<any> {
-  if (!val) return [];
-  if (typeof val === "boolean") return arrayify([val], mapFn);
-  if (typeof val === "string") return arrayify(list(val), mapFn);
-
-  if (Array.isArray(val)) {
-    if (mapFn) val = val.map(mapFn);
-    return val;
-  }
-
-  return [val];
-}
-
-/**
- * Makes boolean-like strings into booleans.
- */
-
-export function booleanify(val: any): boolean | any {
-  if (val === "true" || val == 1) {
-    return true;
-  }
-
-  if (val === "false" || val == 0 || !val) {
-    return false;
-  }
-
-  return val;
-}
-
-/**
- * Tests if a filename should be ignored based on "ignore" and "only" options.
- */
-
-export function shouldIgnore(
-  filename: string,
-  ignore: Array<RegExp | Function>,
-  only?: Array<RegExp | Function>,
-): boolean {
-  filename = filename.replace(/\\/g, "/");
-
-  if (ignore && ignore.length) {
-    for (const pattern of ignore) {
-      if (matchesPattern(pattern, filename)) return true;
-    }
-  }
-
-  if (only) {
-    for (const pattern of only) {
-      if (matchesPattern(pattern, filename)) return false;
-    }
-    return true;
-  }
-
-  return false;
-}
-
-/**
- * Returns result of calling function with filename if pattern is a function.
- * Otherwise returns result of matching pattern Regex with filename.
- */
-
-function matchesPattern(pattern: Function | RegExp, filename: string) {
-  if (typeof pattern === "function") {
-    return pattern(filename);
-  } else {
-    return pattern.test(filename);
-  }
-}
diff --git a/packages/babel-core/test/api.js b/packages/babel-core/test/api.js
index 3d181488c3..6f345592c5 100644
--- a/packages/babel-core/test/api.js
+++ b/packages/babel-core/test/api.js
@@ -6,7 +6,7 @@ import Plugin from "../lib/transformation/plugin";
 import generator from "babel-generator";
 
 function assertIgnored(result) {
-  assert.ok(result.ignored);
+  assert.ok(!result);
 }
 
 function assertNotIgnored(result) {
@@ -496,51 +496,76 @@ describe("api", function () {
   it("ignore option", function () {
     return Promise.all([
       transformAsync("", {
-        ignore: ["node_modules"],
+        ignore: ["/foo"],
         filename: "/foo/node_modules/bar",
       }).then(assertIgnored),
 
       transformAsync("", {
-        ignore: ["foo/node_modules"],
+        ignore: ["/foo/node_modules"],
         filename: "/foo/node_modules/bar",
       }).then(assertIgnored),
 
       transformAsync("", {
-        ignore: ["foo/node_modules/*.bar"],
+        ignore: ["/foo/node_modules/*"],
+        filename: "/foo/node_modules/bar",
+      }).then(assertIgnored),
+
+      transformAsync("", {
+        ignore: ["/foo/**/*"],
+        filename: "/foo/node_modules/bar",
+      }).then(assertIgnored),
+
+      transformAsync("", {
+        ignore: ["/foo/node_modules/*.bar"],
         filename: "/foo/node_modules/foo.bar",
       }).then(assertIgnored),
+
+      transformAsync("", {
+        ignore: ["/foo/node_modules/*.foo"],
+        filename: "/foo/node_modules/foo.bar",
+      }).then(assertNotIgnored),
+
+      transformAsync("", {
+        ignore: ["/bar/**/*"],
+        filename: "/foo/node_modules/foo.bar",
+      }).then(assertNotIgnored),
     ]);
   });
 
   it("only option", function () {
     return Promise.all([
       transformAsync("", {
-        only: ["node_modules"],
+        only: ["/foo"],
         filename: "/foo/node_modules/bar",
       }).then(assertNotIgnored),
 
       transformAsync("", {
-        only: ["foo/node_modules"],
+        only: ["/foo/*"],
         filename: "/foo/node_modules/bar",
       }).then(assertNotIgnored),
 
       transformAsync("", {
-        only: ["foo/node_modules/*.bar"],
+        only: ["/foo/node_modules"],
+        filename: "/foo/node_modules/bar",
+      }).then(assertNotIgnored),
+
+      transformAsync("", {
+        only: ["/foo/node_modules/*.bar"],
         filename: "/foo/node_modules/foo.bar",
       }).then(assertNotIgnored),
 
       transformAsync("", {
-        only: ["node_modules"],
+        only: ["/foo/node_modules"],
         filename: "/foo/node_module/bar",
       }).then(assertIgnored),
 
       transformAsync("", {
-        only: ["foo/node_modules"],
+        only: ["/foo/node_modules"],
         filename: "/bar/node_modules/foo",
       }).then(assertIgnored),
 
       transformAsync("", {
-        only: ["foo/node_modules/*.bar"],
+        only: ["/foo/node_modules/*.bar"],
         filename: "/foo/node_modules/bar.foo",
       }).then(assertIgnored),
     ]);
diff --git a/packages/babel-core/test/config-chain.js b/packages/babel-core/test/config-chain.js
index 0185c783bb..a9cc6bd2e9 100644
--- a/packages/babel-core/test/config-chain.js
+++ b/packages/babel-core/test/config-chain.js
@@ -31,6 +31,8 @@ describe("buildConfigChain", function () {
     process.env.NODE_ENV = oldNodeEnv;
   });
 
+  // TODO: Tests for ignore and only
+
   it("dir1", function () {
     const chain = buildConfigChain({
       filename: fixture("dir1", "src.js"),
diff --git a/packages/babel-core/test/util.js b/packages/babel-core/test/util.js
deleted file mode 100644
index 5d84ad41f6..0000000000
--- a/packages/babel-core/test/util.js
+++ /dev/null
@@ -1,107 +0,0 @@
-import assert from "assert";
-import * as util from "../lib/util";
-import * as t from "babel-types";
-
-describe("util", function () {
-  it("canCompile", function () {
-    assert.ok(util.canCompile("test.js"));
-    assert.ok(util.canCompile("/test.js"));
-    assert.ok(util.canCompile("/scripts/test.js"));
-
-    assert.ok(util.canCompile("test.es6"));
-    assert.ok(util.canCompile("/test.es6"));
-    assert.ok(util.canCompile("/scripts/test.es6"));
-
-    assert.ok(util.canCompile("test.es"));
-    assert.ok(util.canCompile("/test.es"));
-    assert.ok(util.canCompile("/scripts/test.es"));
-
-    assert.ok(util.canCompile("test.jsx"));
-    assert.ok(util.canCompile("/test.jsx"));
-    assert.ok(util.canCompile("/scripts/test.jsx"));
-
-    assert.ok(!util.canCompile("test"));
-    assert.ok(!util.canCompile("test.css"));
-    assert.ok(!util.canCompile("/test.css"));
-    assert.ok(!util.canCompile("/scripts/test.css"));
-  });
-
-  it("list", function () {
-    assert.deepEqual(util.list(undefined), []);
-    assert.deepEqual(util.list(false), []);
-    assert.deepEqual(util.list(null), []);
-    assert.deepEqual(util.list(""), []);
-    assert.deepEqual(util.list("foo"), ["foo"]);
-    assert.deepEqual(util.list("foo,bar"), ["foo", "bar"]);
-    assert.deepEqual(util.list(["foo", "bar"]), ["foo", "bar"]);
-    assert.deepEqual(util.list(/foo/), [/foo/]);
-
-    const date = new Date;
-    assert.deepEqual(util.list(date), [date]);
-  });
-
-  it("arrayify", function () {
-    assert.deepEqual(util.arrayify(undefined), []);
-    assert.deepEqual(util.arrayify(false), []);
-    assert.deepEqual(util.arrayify(null), []);
-    assert.deepEqual(util.arrayify(""), []);
-    assert.deepEqual(util.arrayify("foo"), ["foo"]);
-    assert.deepEqual(util.arrayify("foo,bar"), ["foo", "bar"]);
-    assert.deepEqual(util.arrayify(["foo", "bar"]), ["foo", "bar"]);
-    assert.deepEqual(util.arrayify({ foo: "bar" }), [{ foo: "bar" }]);
-    assert.deepEqual(util.arrayify(function () { return "foo"; })[0](), "foo");
-  });
-
-  it("regexify", function () {
-    assert.deepEqual(util.regexify(undefined), /.^/);
-    assert.deepEqual(util.regexify(false), /.^/);
-    assert.deepEqual(util.regexify(null), /.^/);
-    assert.deepEqual(util.regexify(""), /.^/);
-    assert.deepEqual(util.regexify(["foo", "bar"]), /foo|bar/i);
-    assert.deepEqual(util.regexify("foobar"), /(?:(?=.)foobar)/i);
-    assert.deepEqual(util.regexify(/foobar/), /foobar/);
-
-    assert.ok(util.regexify("foo/bar").test("bar/foo/bar"));
-    assert.ok(util.regexify("foo/*").test("foo/bar.js"));
-    assert.ok(util.regexify("*.js").test("bar.js"));
-    assert.ok(util.regexify("./foo").test("foo"));
-    assert.ok(util.regexify("./foo/bar.js").test("foo/bar.js"));
-    assert.ok(util.regexify("foobar").test("foobar"));
-
-    assert.throws(function () {
-      util.regexify({});
-    }, /illegal type for regexify/);
-  });
-
-  it("booleanify", function () {
-    assert.strictEqual(util.booleanify("true"), true);
-    assert.strictEqual(util.booleanify("false"), false);
-    assert.strictEqual(util.booleanify("inline"), "inline");
-  });
-
-  it("toIdentifier", function () {
-    assert.equal(t.toIdentifier("swag-lord"), "swagLord");
-  });
-
-  it("shouldIgnore", function () {
-    const reIgnore = /\-reIgnore\.js/;
-    const fnIgnore = function (src) {
-      if (src.indexOf("fnIgnore") > 0) {
-        return true;
-      }
-    };
-
-    assert.equal(util.shouldIgnore("test.js", []), false);
-    assert.equal(util.shouldIgnore("test-reIgnore.js", [fnIgnore]), false);
-    assert.equal(util.shouldIgnore("test-reIgnore.js", [reIgnore]), true);
-
-    assert.equal(util.shouldIgnore("test-fnIgnore.js", [fnIgnore]), true);
-    assert.equal(util.shouldIgnore("test-fnIgnore.js", [reIgnore]), false);
-
-    assert.equal(util.shouldIgnore("test-reIgnore.js", [], [fnIgnore]), true);
-    assert.equal(util.shouldIgnore("test-reIgnore.js", [], [reIgnore]), false);
-
-    assert.equal(util.shouldIgnore("test-fnIgnore.js", [], [fnIgnore]), false);
-    assert.equal(util.shouldIgnore("test-fnIgnore.js", [], [reIgnore]), true);
-  });
-});
diff --git a/packages/babel-register/src/node.js b/packages/babel-register/src/node.js
index 229ecb3475..3ae82ad886 100644
--- a/packages/babel-register/src/node.js
+++ b/packages/babel-register/src/node.js
@@ -1,9 +1,10 @@
 import deepClone from "lodash/cloneDeep";
 import sourceMapSupport from "source-map-support";
 import * as registerCache from "./cache";
+import escapeRegExp from "lodash/escapeRegExp";
 import extend from "lodash/extend";
 import * as babel from "babel-core";
-import { util, OptionManager } from "babel-core";
+import { OptionManager, DEFAULT_EXTENSIONS } from "babel-core";
 import fs from "fs";
 import path from "path";
 
@@ -28,18 +29,9 @@ let cache = registerCache.get();
 
 const transformOpts = {};
 
-let ignore;
-let only;
-
 let oldHandlers = {};
 const maps = {};
 
-const cwd = process.cwd();
-
-function getRelativePath(filename) {
-  return path.relative(cwd, filename);
-}
-
 function mtime(filename) {
   return +fs.statSync(filename).mtime;
 }
@@ -54,6 +46,9 @@ function compile(filename) {
     { filename }
   ));
 
+  // Bail out ASAP if the file has been ignored.
+  if (opts === null) return null;
+
   let cacheKey = `${JSON.stringify(opts)}:${babel.version}`;
 
   const env = babel.getEnv(false);
@@ -87,27 +82,14 @@ function compile(filename) {
   return result.code;
 }
 
-function shouldIgnore(filename) {
-  if (!ignore && !only) {
-    return getRelativePath(filename).split(path.sep).indexOf("node_modules") >= 0;
-  } else {
-    return util.shouldIgnore(filename, ignore || [], only);
-  }
-}
-
-function loader(m, filename) {
-  m._compile(compile(filename), filename);
-}
-
 function registerExtension(ext) {
   const old = oldHandlers[ext] || oldHandlers[".js"] || require.extensions[".js"];
 
   require.extensions[ext] = function (m, filename) {
-    if (shouldIgnore(filename)) {
-      old(m, filename);
-    } else {
-      loader(m, filename, old);
-    }
+    const result = compile(filename);
+
+    if (result === null) old(m, filename);
+    else m._compile(result, filename);
   };
 }
 
@@ -129,20 +111,27 @@ function hookExtensions(_exts) {
   });
 }
 
-hookExtensions(util.canCompile.EXTENSIONS);
+hookExtensions(DEFAULT_EXTENSIONS);
 
 export default function (opts?: Object = {}) {
-  if (opts.only != null) only = util.arrayify(opts.only, util.regexify);
-  if (opts.ignore != null) ignore = util.arrayify(opts.ignore, util.regexify);
-
-  if (opts.extensions) hookExtensions(util.arrayify(opts.extensions));
+  if (opts.extensions) hookExtensions(opts.extensions);
 
   if (opts.cache === false) cache = null;
 
   delete opts.extensions;
-  delete opts.ignore;
   delete opts.cache;
-  delete opts.only;
 
   extend(transformOpts, opts);
+
+  if (!transformOpts.ignore && !transformOpts.only) {
+    // By default, ignore files inside the node_modules relative to the current working directory.
+    transformOpts.ignore = [
+      new RegExp(
+        "^" +
+        escapeRegExp(process.cwd() + path.sep) +
+        ".*" +
+        escapeRegExp(path.sep + "node_modules" + path.sep)
+      , "i"),
+    ];
+  }
 }
diff --git a/packages/babel-types/test/converters.js b/packages/babel-types/test/converters.js
index d787265a7f..43e1e887a7 100644
--- a/packages/babel-types/test/converters.js
+++ b/packages/babel-types/test/converters.js
@@ -2,6 +2,10 @@ import * as t from "../lib";
 import { assert } from "chai";
 
 describe("converters", function () {
+  it("toIdentifier", function () {
+    assert.equal(t.toIdentifier("swag-lord"), "swagLord");
+  });
+
   describe("valueToNode", function () {
     it("number", function () {
       assert.deepEqual(t.valueToNode(Math.PI), t.numericLiteral(Math.PI));