diff --git a/packages/babel-cli/bin/babel/dir.js b/packages/babel-cli/bin/babel/dir.js
index 7a19d53063..6e0e0cd65d 100644
--- a/packages/babel-cli/bin/babel/dir.js
+++ b/packages/babel-cli/bin/babel/dir.js
@@ -28,6 +28,8 @@ module.exports = function (commander, filenames, opts) {
   };
 
   var handleFile = function (src, filename) {
+    if (util.shouldIgnore(src)) return;
+
     if (util.canCompile(filename)) {
       write(src, filename);
     } else if (commander.copyFiles) {
diff --git a/packages/babel-cli/bin/babel/file.js b/packages/babel-cli/bin/babel/file.js
index f61efde461..9e4990e289 100644
--- a/packages/babel-cli/bin/babel/file.js
+++ b/packages/babel-cli/bin/babel/file.js
@@ -107,6 +107,8 @@ module.exports = function (commander, filenames, opts) {
     });
 
     _.each(_filenames, function (filename) {
+      if (!util.shouldIgnore(filename)) return;
+
       results.push(util.compile(filename));
     });
 
diff --git a/packages/babel-cli/bin/babel/index.js b/packages/babel-cli/bin/babel/index.js
index 04a61612fd..48b214d0a8 100755
--- a/packages/babel-cli/bin/babel/index.js
+++ b/packages/babel-cli/bin/babel/index.js
@@ -102,12 +102,15 @@ if (errors.length) {
 
 //
 
-exports.opts = {};
+var opts = exports.opts = {};
 
 each(options, function (opt, key) {
-  exports.opts[key] = commander[key];
+  opts[key] = commander[key];
 });
 
+opts.ignore = util.arrayify(opts.ignore, util.regexify);
+opts.only   = util.arrayify(opts.only, util.regexify);
+
 var fn;
 
 if (commander.outDir) {
diff --git a/packages/babel-cli/bin/babel/util.js b/packages/babel-cli/bin/babel/util.js
index a7a640285c..1de4d894db 100644
--- a/packages/babel-cli/bin/babel/util.js
+++ b/packages/babel-cli/bin/babel/util.js
@@ -16,6 +16,10 @@ exports.readdir = readdir;
 
 exports.canCompile = util.canCompile;
 
+exports.shouldIgnore = function (loc) {
+  return util.shouldIgnore(loc, index.opts.ignore, index.opts.only);
+};
+
 exports.addSourceMappingUrl = function (code, loc) {
   return code + "\n//# sourceMappingURL=" + path.basename(loc);
 };
@@ -23,6 +27,8 @@ exports.addSourceMappingUrl = function (code, loc) {
 exports.transform = function (filename, code, opts) {
   opts = _.defaults(opts || {}, index.opts);
   opts.filename = filename;
+  opts.ignore = null;
+  opts.only = null;
 
   var result = babel.transform(code, opts);
   result.filename = filename;
diff --git a/src/babel/transformation/file/index.js b/src/babel/transformation/file/index.js
index eaa53be048..56026f03d0 100644
--- a/src/babel/transformation/file/index.js
+++ b/src/babel/transformation/file/index.js
@@ -422,23 +422,7 @@ export default class File {
 
   shouldIgnore() {
     var opts = this.opts;
-
-    var filename = opts.filename;
-    var ignore   = opts.ignore;
-    var only     = opts.only;
-
-    if (only.length) {
-      for (var i = 0; i < only.length; i++) {
-        if (only[i].test(filename)) return false;
-      }
-      return true;
-    } else if (ignore.length) {
-      for (var i = 0; i < ignore.length; i++) {
-        if (ignore[i].test(filename)) return true;
-      }
-    }
-
-    return false;
+    return util.shouldIgnore(opts.filename, opts.ignore, opts.only);
   }
 
   parse(code: string) {
diff --git a/src/babel/util.js b/src/babel/util.js
index f0bbc4286c..298267bf59 100644
--- a/src/babel/util.js
+++ b/src/babel/util.js
@@ -93,6 +93,21 @@ export function booleanify(val: any): boolean {
   return val;
 }
 
+export function shouldIgnore(filename, ignore, only) {
+  if (only.length) {
+    for (var i = 0; i < only.length; i++) {
+      if (only[i].test(filename)) return false;
+    }
+    return true;
+  } else if (ignore.length) {
+    for (var i = 0; i < ignore.length; i++) {
+      if (ignore[i].test(filename)) return true;
+    }
+  }
+
+  return false;
+}
+
 var templateVisitor = {
   enter(node, parent, scope, nodes) {
     if (t.isExpressionStatement(node)) {
diff --git a/test/core/fixtures/bin/babel/--ignore/in-files/src/bar/index.js b/test/core/fixtures/bin/babel/--ignore/in-files/src/bar/index.js
new file mode 100644
index 0000000000..e46160df1c
--- /dev/null
+++ b/test/core/fixtures/bin/babel/--ignore/in-files/src/bar/index.js
@@ -0,0 +1 @@
+bar;
diff --git a/test/core/fixtures/bin/babel/--ignore/in-files/src/foo/foo.js b/test/core/fixtures/bin/babel/--ignore/in-files/src/foo/foo.js
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/test/core/fixtures/bin/babel/--ignore/options.json b/test/core/fixtures/bin/babel/--ignore/options.json
new file mode 100644
index 0000000000..1911426f62
--- /dev/null
+++ b/test/core/fixtures/bin/babel/--ignore/options.json
@@ -0,0 +1,3 @@
+{
+  "args": ["src", "--out-dir", "lib", "--ignore", "src/foo/*"]
+}
diff --git a/test/core/fixtures/bin/babel/--ignore/stdout.txt b/test/core/fixtures/bin/babel/--ignore/stdout.txt
new file mode 100644
index 0000000000..1eb8f922d1
--- /dev/null
+++ b/test/core/fixtures/bin/babel/--ignore/stdout.txt
@@ -0,0 +1 @@
+src/bar/index.js -> lib/bar/index.js
diff --git a/test/core/fixtures/bin/babel/--only/in-files/src/bar/index.js b/test/core/fixtures/bin/babel/--only/in-files/src/bar/index.js
new file mode 100644
index 0000000000..e46160df1c
--- /dev/null
+++ b/test/core/fixtures/bin/babel/--only/in-files/src/bar/index.js
@@ -0,0 +1 @@
+bar;
diff --git a/test/core/fixtures/bin/babel/--only/in-files/src/foo/index.js b/test/core/fixtures/bin/babel/--only/in-files/src/foo/index.js
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/test/core/fixtures/bin/babel/--only/options.json b/test/core/fixtures/bin/babel/--only/options.json
new file mode 100644
index 0000000000..7b05f3fb82
--- /dev/null
+++ b/test/core/fixtures/bin/babel/--only/options.json
@@ -0,0 +1,3 @@
+{
+  "args": ["src", "--out-dir", "lib", "--only", "src/bar/*"]
+}
diff --git a/test/core/fixtures/bin/babel/--only/stdout.txt b/test/core/fixtures/bin/babel/--only/stdout.txt
new file mode 100644
index 0000000000..1eb8f922d1
--- /dev/null
+++ b/test/core/fixtures/bin/babel/--only/stdout.txt
@@ -0,0 +1 @@
+src/bar/index.js -> lib/bar/index.js