diff --git a/packages/babel-cli/src/babel/dir.js b/packages/babel-cli/src/babel/dir.js
index 0316062590..7a19148bd7 100644
--- a/packages/babel-cli/src/babel/dir.js
+++ b/packages/babel-cli/src/babel/dir.js
@@ -1,3 +1,4 @@
+import defaults from "lodash/defaults";
 import outputFileSync from "output-file-sync";
 import slash from "slash";
 import path from "path";
@@ -5,17 +6,17 @@ import fs from "fs";
 
 import * as util from "./util";
 
-export default function (commander, filenames) {
+export default function (commander, filenames, opts) {
   function write(src, relative) {
     // remove extension and then append back on .js
     relative = relative.replace(/\.(\w*?)$/, "") + ".js";
 
     const dest = path.join(commander.outDir, relative);
 
-    const data = util.compile(src, {
+    const data = util.compile(src, defaults({
       sourceFileName: slash(path.relative(dest + "/..", src)),
       sourceMapTarget: path.basename(relative),
-    });
+    }, opts));
     if (!commander.copyFiles && data.ignored) return;
 
     // we've requested explicit sourcemaps to be written to disk
@@ -32,7 +33,7 @@ export default function (commander, filenames) {
   }
 
   function handleFile(src, filename) {
-    if (util.shouldIgnore(src)) return;
+    if (util.shouldIgnore(src, opts)) return;
 
     if (util.canCompile(filename, commander.extensions)) {
       write(src, filename);
diff --git a/packages/babel-cli/src/babel/file.js b/packages/babel-cli/src/babel/file.js
index fb4b1f9a0c..181432c1e6 100644
--- a/packages/babel-cli/src/babel/file.js
+++ b/packages/babel-cli/src/babel/file.js
@@ -1,4 +1,5 @@
 import convertSourceMap from "convert-source-map";
+import defaults from "lodash/defaults";
 import sourceMap from "source-map";
 import slash from "slash";
 import path from "path";
@@ -96,9 +97,9 @@ export default function (commander, filenames, opts) {
     });
 
     process.stdin.on("end", function () {
-      results.push(util.transform(commander.filename, code, {
+      results.push(util.transform(commander.filename, code, defaults({
         sourceFileName: "stdin",
-      }));
+      }, opts)));
       output();
     });
   };
@@ -123,7 +124,7 @@ export default function (commander, filenames, opts) {
     });
 
     _filenames.forEach(function (filename) {
-      if (util.shouldIgnore(filename)) return;
+      if (util.shouldIgnore(filename, opts)) return;
 
       let sourceFilename = filename;
       if (commander.outFile) {
@@ -131,9 +132,9 @@ export default function (commander, filenames, opts) {
       }
       sourceFilename = slash(sourceFilename);
 
-      const data = util.compile(filename, {
+      const data = util.compile(filename, defaults({
         sourceFileName: sourceFilename,
-      });
+      }, opts));
 
       if (data.ignored) return;
       results.push(data);
@@ -158,7 +159,7 @@ export default function (commander, filenames, opts) {
           pollInterval: 10,
         },
       }).on("all", function (type, filename) {
-        if (util.shouldIgnore(filename) || !util.canCompile(filename, commander.extensions)) return;
+        if (util.shouldIgnore(filename, opts) || !util.canCompile(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 a96056b3dc..8d39e17e5d 100755
--- a/packages/babel-cli/src/babel/index.js
+++ b/packages/babel-cli/src/babel/index.js
@@ -106,7 +106,7 @@ if (errors.length) {
 
 //
 
-export const opts = {};
+const opts = {};
 
 Object.keys(options).forEach(function (key) {
   const opt = options[key];
diff --git a/packages/babel-cli/src/babel/util.js b/packages/babel-cli/src/babel/util.js
index e92b09c671..d95555ae1d 100644
--- a/packages/babel-cli/src/babel/util.js
+++ b/packages/babel-cli/src/babel/util.js
@@ -1,12 +1,9 @@
 import commander from "commander";
-import defaults from "lodash/defaults";
 import readdir from "fs-readdir-recursive";
 import * as babel from "babel-core";
 import path from "path";
 import fs from "fs";
 
-import * as index from "./index";
-
 export function chmod(src, dest) {
   fs.chmodSync(dest, fs.statSync(src).mode);
 }
@@ -21,8 +18,8 @@ export { readdir };
 
 export const canCompile = babel.util.canCompile;
 
-export function shouldIgnore(loc) {
-  return babel.util.shouldIgnore(loc, index.opts.ignore, index.opts.only);
+export function shouldIgnore(loc, opts) {
+  return babel.util.shouldIgnore(loc, opts.ignore, opts.only);
 }
 
 export function addSourceMappingUrl(code, loc) {
@@ -34,8 +31,9 @@ export function log(msg) {
 }
 
 export function transform(filename, code, opts) {
-  opts = defaults(opts || {}, index.opts);
-  opts.filename = filename;
+  opts = Object.assign({}, opts, {
+    filename,
+  });
 
   const result = babel.transform(code, opts);
   result.filename = filename;