diff --git a/packages/jest-haste-map/src/__tests__/index.test.js b/packages/jest-haste-map/src/__tests__/index.test.js
index 5d67e670dcde..1135360eb698 100644
--- a/packages/jest-haste-map/src/__tests__/index.test.js
+++ b/packages/jest-haste-map/src/__tests__/index.test.js
@@ -294,6 +294,45 @@ describe('HasteMap', () => {
     });
   });
 
+  it('ignores vcs directories without ignore pattern', () => {
+    mockFs['/project/fruits/.git/fruit-history.js'] = `
+      // test
+    `;
+    return new HasteMap(defaultConfig).build().then(({hasteFS}) => {
+      expect(hasteFS.matchFiles('.git')).toEqual([]);
+    });
+  });
+
+  it('ignores vcs directories with ignore pattern regex', () => {
+    const config = {...defaultConfig, ignorePattern: /Kiwi/};
+    mockFs['/project/fruits/Kiwi.js'] = `
+      // Kiwi!
+    `;
+
+    mockFs['/project/fruits/.git/fruit-history.js'] = `
+      // test
+    `;
+    return new HasteMap(config).build().then(({hasteFS}) => {
+      expect(hasteFS.matchFiles(/Kiwi/)).toEqual([]);
+      expect(hasteFS.matchFiles('.git')).toEqual([]);
+    });
+  });
+
+  it('ignores vcs directories with ignore pattern function', () => {
+    const config = {...defaultConfig, ignorePattern: f => /Kiwi/.test(f)};
+    mockFs['/project/fruits/Kiwi.js'] = `
+      // Kiwi!
+    `;
+
+    mockFs['/project/fruits/.git/fruit-history.js'] = `
+      // test
+    `;
+    return new HasteMap(config).build().then(({hasteFS}) => {
+      expect(hasteFS.matchFiles(/Kiwi/)).toEqual([]);
+      expect(hasteFS.matchFiles('.git')).toEqual([]);
+    });
+  });
+
   it('builds a haste map on a fresh cache', () => {
     // Include these files in the map
     mockFs['/project/fruits/node_modules/react/React.js'] = `
diff --git a/packages/jest-haste-map/src/index.ts b/packages/jest-haste-map/src/index.ts
index 572164a4bbf2..23afea055f1a 100644
--- a/packages/jest-haste-map/src/index.ts
+++ b/packages/jest-haste-map/src/index.ts
@@ -113,6 +113,9 @@ const CHANGE_INTERVAL = 30;
 const MAX_WAIT_TIME = 240000;
 const NODE_MODULES = path.sep + 'node_modules' + path.sep;
 const PACKAGE_JSON = path.sep + 'package.json';
+const VCS_DIRECTORIES = ['.git', '.svn', '.hg']
+  .map(vcs => path.sep + vcs + path.sep)
+  .join('|');
 
 // TypeScript doesn't like us importing from outside `rootDir`, but it doesn't
 // understand `require`.
@@ -233,7 +236,6 @@ class HasteMap extends EventEmitter {
       extensions: options.extensions,
       forceNodeFilesystemAPI: !!options.forceNodeFilesystemAPI,
       hasteImplModulePath: options.hasteImplModulePath,
-      ignorePattern: options.ignorePattern,
       maxWorkers: options.maxWorkers,
       mocksPattern: options.mocksPattern
         ? new RegExp(options.mocksPattern)
@@ -250,11 +252,24 @@ class HasteMap extends EventEmitter {
       watch: !!options.watch,
     };
     this._console = options.console || global.console;
-    if (options.ignorePattern && !(options.ignorePattern instanceof RegExp)) {
-      this._console.warn(
-        'jest-haste-map: the `ignorePattern` options as a function is being ' +
-          'deprecated. Provide a RegExp instead. See https://github.com/facebook/jest/pull/4063.',
-      );
+
+    if (options.ignorePattern) {
+      if (options.ignorePattern instanceof RegExp) {
+        this._options.ignorePattern = new RegExp(
+          options.ignorePattern.source.concat('|' + VCS_DIRECTORIES),
+        );
+      } else {
+        const ignorePattern = options.ignorePattern;
+        this._options.ignorePattern = (filePath: string) =>
+          new RegExp(VCS_DIRECTORIES).test(filePath) || ignorePattern(filePath);
+
+        this._console.warn(
+          'jest-haste-map: the `ignorePattern` options as a function is being ' +
+            'deprecated. Provide a RegExp instead. See https://github.com/facebook/jest/pull/4063.',
+        );
+      }
+    } else {
+      this._options.ignorePattern = new RegExp(VCS_DIRECTORIES);
     }
 
     const rootDirHash = createHash('md5').update(options.rootDir).digest('hex');