diff --git a/packages/babel-cli/src/babel/dir.js b/packages/babel-cli/src/babel/dir.js
index 1dbd0ed129..2eaca85750 100644
--- a/packages/babel-cli/src/babel/dir.js
+++ b/packages/babel-cli/src/babel/dir.js
@@ -89,7 +89,7 @@ export default async function({ cliOptions, babelOptions }) {
 
     const stat = fs.statSync(filenameOrDir);
 
-    if (stat.isDirectory(filenameOrDir)) {
+    if (stat.isDirectory()) {
       const dirname = filenameOrDir;
 
       let count = 0;
diff --git a/packages/babel-cli/src/babel/util.js b/packages/babel-cli/src/babel/util.js
index 5d0cdc479e..b2d22a3f77 100644
--- a/packages/babel-cli/src/babel/util.js
+++ b/packages/babel-cli/src/babel/util.js
@@ -15,11 +15,15 @@ export function readdir(
   includeDotfiles: boolean,
   filter: ReaddirFilter,
 ) {
-  return readdirRecursive(
-    dirname,
-    filename =>
-      (includeDotfiles || filename[0] !== ".") && (!filter || filter(filename)),
-  );
+  return readdirRecursive(dirname, (filename, _index, currentDirectory) => {
+    const stat = fs.statSync(path.join(currentDirectory, filename));
+
+    if (stat.isDirectory()) return true;
+
+    return (
+      (includeDotfiles || filename[0] !== ".") && (!filter || filter(filename))
+    );
+  });
 }
 
 export function readdirForCompilable(
diff --git a/packages/babel-cli/test/fixtures/babel/dir --out-file/in-files/src/bar/bar.js b/packages/babel-cli/test/fixtures/babel/dir --out-file/in-files/src/bar/bar.js
new file mode 100644
index 0000000000..9e99278492
--- /dev/null
+++ b/packages/babel-cli/test/fixtures/babel/dir --out-file/in-files/src/bar/bar.js	
@@ -0,0 +1 @@
+ (() => 42)
\ No newline at end of file
diff --git a/packages/babel-cli/test/fixtures/babel/dir --out-file/in-files/src/foo.js b/packages/babel-cli/test/fixtures/babel/dir --out-file/in-files/src/foo.js
new file mode 100644
index 0000000000..4bc9539528
--- /dev/null
+++ b/packages/babel-cli/test/fixtures/babel/dir --out-file/in-files/src/foo.js	
@@ -0,0 +1 @@
+arr.map(x => x * MULTIPLIER);
diff --git a/packages/babel-cli/test/fixtures/babel/dir --out-file/options.json b/packages/babel-cli/test/fixtures/babel/dir --out-file/options.json
new file mode 100644
index 0000000000..b82e32da5b
--- /dev/null
+++ b/packages/babel-cli/test/fixtures/babel/dir --out-file/options.json	
@@ -0,0 +1,3 @@
+{
+  "args": ["src", "--out-file", "test.js"]
+}
diff --git a/packages/babel-cli/test/fixtures/babel/dir --out-file/out-files/test.js b/packages/babel-cli/test/fixtures/babel/dir --out-file/out-files/test.js
new file mode 100644
index 0000000000..d3e579815a
--- /dev/null
+++ b/packages/babel-cli/test/fixtures/babel/dir --out-file/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/stdout.txt b/packages/babel-cli/test/fixtures/babel/dir --out-file/stdout.txt
new file mode 100644
index 0000000000..e69de29bb2