diff --git a/packages/babel-cli/src/babel/file.js b/packages/babel-cli/src/babel/file.js
index 31433b33da..f0678e27ed 100644
--- a/packages/babel-cli/src/babel/file.js
+++ b/packages/babel-cli/src/babel/file.js
@@ -137,7 +137,11 @@ export default async function({ cliOptions, babelOptions }) {
         const dirname = filename;
 
         util
-          .readdirForCompilable(filename, cliOptions.includeDotfiles)
+          .readdirForCompilable(
+            filename,
+            cliOptions.includeDotfiles,
+            cliOptions.extensions,
+          )
           .forEach(function(filename) {
             _filenames.push(path.join(dirname, filename));
           });
diff --git a/packages/babel-cli/src/babel/util.js b/packages/babel-cli/src/babel/util.js
index ad972fd0cd..99c9ae9b00 100644
--- a/packages/babel-cli/src/babel/util.js
+++ b/packages/babel-cli/src/babel/util.js
@@ -29,8 +29,11 @@ export function readdir(
 export function readdirForCompilable(
   dirname: string,
   includeDotfiles: boolean,
+  altExts?: Array<string>,
 ) {
-  return readdir(dirname, includeDotfiles, isCompilableExtension);
+  return readdir(dirname, includeDotfiles, function(filename) {
+    return isCompilableExtension(filename, altExts);
+  });
 }
 
 /**
diff --git a/packages/babel-cli/test/fixtures/babel/dir --out-file --extensions/in-files/src/bar/bar.es b/packages/babel-cli/test/fixtures/babel/dir --out-file --extensions/in-files/src/bar/bar.es
new file mode 100644
index 0000000000..9e99278492
--- /dev/null
+++ b/packages/babel-cli/test/fixtures/babel/dir --out-file --extensions/in-files/src/bar/bar.es	
@@ -0,0 +1 @@
+ (() => 42)
\ No newline at end of file
diff --git a/packages/babel-cli/test/fixtures/babel/dir --out-file --extensions/in-files/src/foo.es b/packages/babel-cli/test/fixtures/babel/dir --out-file --extensions/in-files/src/foo.es
new file mode 100644
index 0000000000..4bc9539528
--- /dev/null
+++ b/packages/babel-cli/test/fixtures/babel/dir --out-file --extensions/in-files/src/foo.es	
@@ -0,0 +1 @@
+arr.map(x => x * MULTIPLIER);
diff --git a/packages/babel-cli/test/fixtures/babel/dir --out-file --extensions/options.json b/packages/babel-cli/test/fixtures/babel/dir --out-file --extensions/options.json
new file mode 100644
index 0000000000..cb501c3b85
--- /dev/null
+++ b/packages/babel-cli/test/fixtures/babel/dir --out-file --extensions/options.json	
@@ -0,0 +1,3 @@
+{
+  "args": ["src", "--out-file", "test.js", "--extensions", ".es"]
+}
diff --git a/packages/babel-cli/test/fixtures/babel/dir --out-file --extensions/out-files/test.js b/packages/babel-cli/test/fixtures/babel/dir --out-file --extensions/out-files/test.js
new file mode 100644
index 0000000000..d3e579815a
--- /dev/null
+++ b/packages/babel-cli/test/fixtures/babel/dir --out-file --extensions/out-files/test.js	
@@ -0,0 +1,10 @@
+"use strict";
+
+(function () {
+  return 42;
+});
+"use strict";
+
+arr.map(function (x) {
+  return x * MULTIPLIER;
+});
diff --git a/packages/babel-cli/test/fixtures/babel/dir --out-file --extensions/stdout.txt b/packages/babel-cli/test/fixtures/babel/dir --out-file --extensions/stdout.txt
new file mode 100644
index 0000000000..e69de29bb2