diff --git a/packages/aws-cdk/lib/init.ts b/packages/aws-cdk/lib/init.ts
index 1937ddf46e122..f0475873c3691 100644
--- a/packages/aws-cdk/lib/init.ts
+++ b/packages/aws-cdk/lib/init.ts
@@ -208,7 +208,7 @@ async function initializeProject(template: InitTemplate, language: string, canUs
 
 async function assertIsEmptyDirectory() {
   const files = await fs.readdir(process.cwd());
-  if (files.length !== 0) {
+  if (files.filter(f => !f.startsWith('.')).length !== 0) {
     throw new Error('`cdk init` cannot be run in a non-empty directory!');
   }
 }
diff --git a/packages/aws-cdk/test/test.init.ts b/packages/aws-cdk/test/test.init.ts
index 10da8c23535b2..694327ca8dccd 100644
--- a/packages/aws-cdk/test/test.init.ts
+++ b/packages/aws-cdk/test/test.init.ts
@@ -45,6 +45,18 @@ export = {
     test.equal(true, await fs.pathExists('package.json'));
     test.equal(true, await fs.pathExists('bin'));
 
+    test.done();
+  },
+
+  async 'git directory does not throw off the initer!'(test: Test) {
+    fs.mkdirSync('.git');
+
+    await cliInit('app', 'typescript', false);
+
+    // Check that package.json and bin/ got created in the current directory
+    test.equal(true, await fs.pathExists('package.json'));
+    test.equal(true, await fs.pathExists('bin'));
+
     test.done();
   }
 };