diff --git a/packages/babel-cli/bin/babel/dir.js b/packages/babel-cli/bin/babel/dir.js
index 780ac71958..6c7b2f41cc 100644
--- a/packages/babel-cli/bin/babel/dir.js
+++ b/packages/babel-cli/bin/babel/dir.js
@@ -16,6 +16,7 @@ module.exports = function (commander, filenames, opts) {
     var data = util.compile(src, {
       sourceFileName: slash(path.relative(dest + "/..", src))
     });
+    if (data.ignored) return;
 
     if (commander.sourceMaps && commander.sourceMaps !== "inline") {
       var mapLoc = dest + ".map";
diff --git a/packages/babel-cli/bin/babel/file.js b/packages/babel-cli/bin/babel/file.js
index 0764db9908..7830fb67b4 100644
--- a/packages/babel-cli/bin/babel/file.js
+++ b/packages/babel-cli/bin/babel/file.js
@@ -116,7 +116,9 @@ module.exports = function (commander, filenames, opts) {
     _.each(_filenames, function (filename) {
       if (util.shouldIgnore(filename)) return;
 
-      results.push(util.compile(filename));
+      var data = util.compile(filename);
+      if (data.ignored) return;
+      results.push(data);
     });
 
     output();
diff --git a/src/babel/transformation/file/index.js b/src/babel/transformation/file/index.js
index c030070379..95bdb2ef11 100644
--- a/src/babel/transformation/file/index.js
+++ b/src/babel/transformation/file/index.js
@@ -493,6 +493,7 @@ export default class File {
       if (this.shouldIgnore()) {
         return {
           metadata: {},
+          ignored:  true,
           code:     code,
           map:      null,
           ast:      null