diff --git a/integration_tests/__tests__/runtime-internal-module-registry-test.js b/integration_tests/__tests__/runtime-internal-module-registry-test.js
new file mode 100644
index 000000000000..89fbe6a44b11
--- /dev/null
+++ b/integration_tests/__tests__/runtime-internal-module-registry-test.js
@@ -0,0 +1,33 @@
+/**
+ * Copyright (c) 2014-present, Facebook, Inc. All rights reserved.
+ *
+ * This source code is licensed under the BSD-style license found in the
+ * LICENSE file in the root directory of this source tree. An additional grant
+ * of patent rights can be found in the PATENTS file in the same directory.
+ *
+ * @emails oncall+jsinfra
+ */
+'use strict';
+
+const runJest = require('../runJest');
+
+describe('Runtime Internal Module Registry', () => {
+  // Previously, if Jest required a module (e.g. requiring `mkdirp` from
+  // `jest-util`) and the project *using* Jest also required that module, Jest
+  // wouldn't re-require it and thus ignored any mocks that the module may have
+  // used.
+  //
+  // This test verifies that that behavior doesn't happen anymore, and correctly
+  // uses two module registries: an internal registry that's used specificly by
+  // Jest to require any internal modules used when setting up the test
+  // environment, and a "normal" module registry that's used by the actual test
+  // code (and can safely be cleared after every test)
+  it('correctly makes use of internal module registry when requiring modules',
+    () => {
+      const {json} = runJest.json('runtime-internal-module-registry', []);
+
+      expect(json.numTotalTests).toBe(1);
+      expect(json.numPassedTests).toBe(1);
+    }
+  );
+});
diff --git a/integration_tests/runtime-internal-module-registry/__mocks__/fs.js b/integration_tests/runtime-internal-module-registry/__mocks__/fs.js
new file mode 100644
index 000000000000..0f30b438a389
--- /dev/null
+++ b/integration_tests/runtime-internal-module-registry/__mocks__/fs.js
@@ -0,0 +1,25 @@
+/**
+ * Copyright (c) 2014-present, Facebook, Inc. All rights reserved.
+ *
+ * This source code is licensed under the BSD-style license found in the
+ * LICENSE file in the root directory of this source tree. An additional grant
+ * of patent rights can be found in the PATENTS file in the same directory.
+ */
+
+'use strict';
+
+const fs = jest.genMockFromModule('fs');
+
+let mkdirWasCalled = false;
+
+function mkdirSync() {
+  mkdirWasCalled = true;
+  return;
+}
+
+fs.mkdirSync = mkdirSync;
+fs.__wasMkdirCalled = function() {
+  return mkdirWasCalled;
+};
+
+module.exports = fs;
diff --git a/integration_tests/runtime-internal-module-registry/__tests__/runtime-internal-module-registry-test.js b/integration_tests/runtime-internal-module-registry/__tests__/runtime-internal-module-registry-test.js
new file mode 100644
index 000000000000..3150859d81c6
--- /dev/null
+++ b/integration_tests/runtime-internal-module-registry/__tests__/runtime-internal-module-registry-test.js
@@ -0,0 +1,28 @@
+/**
+ * Copyright (c) 2014-present, Facebook, Inc. All rights reserved.
+ *
+ * This source code is licensed under the BSD-style license found in the
+ * LICENSE file in the root directory of this source tree. An additional grant
+ * of patent rights can be found in the PATENTS file in the same directory.
+ */
+
+'use strict';
+
+jest.mock('fs');
+
+describe('Runtime internal module registry', () => {
+  it('behaves correctly when requiring a module that is used by jest internals', () => {
+    const fs = require('fs');
+
+    // We require from this crazy path so that we can mimick Jest (and it's
+    // transitive deps) being installed along side a projects deps (e.g. with an
+    // NPM3 flat dep tree)
+    const jestUtil = require('../../../packages/jest-util');
+
+    // If FS is mocked correctly, this folder won't actually be created on the
+    // filesystem
+    jestUtil.createDirectory('./dont-create-this-folder');
+
+    expect(fs.__wasMkdirCalled()).toBe(true);
+  });
+});
diff --git a/integration_tests/runtime-internal-module-registry/package.json b/integration_tests/runtime-internal-module-registry/package.json
new file mode 100644
index 000000000000..148788b25446
--- /dev/null
+++ b/integration_tests/runtime-internal-module-registry/package.json
@@ -0,0 +1,5 @@
+{
+  "jest": {
+    "testEnvironment": "node"
+  }
+}
diff --git a/packages/jest-runtime/src/index.js b/packages/jest-runtime/src/index.js
index 510f57949a79..98695477d51f 100644
--- a/packages/jest-runtime/src/index.js
+++ b/packages/jest-runtime/src/index.js
@@ -81,6 +81,7 @@ class Runtime {
   _mockRegistry: {[key: string]: any};
   _mocksPattern: ?RegExp;
   _moduleRegistry: {[key: string]: Module};
+  _internalModuleRegistry: {[key: string]: Module};
   _resolver: Resolver;
   _shouldAutoMock: boolean;
   _shouldMockModuleCache: BooleanObject;
@@ -96,6 +97,7 @@ class Runtime {
     resolver: Resolver,
   ) {
     this._moduleRegistry = Object.create(null);
+    this._internalModuleRegistry = Object.create(null);
     this._mockRegistry = Object.create(null);
     this._config = config;
     this._environment = environment;
@@ -225,6 +227,10 @@ class Runtime {
     const moduleID = this._normalizeID(from, moduleName);
     let modulePath;
 
+    const moduleRegistry = (!options || !options.isInternalModule) ?
+      this._moduleRegistry :
+      this._internalModuleRegistry;
+
     // Some old tests rely on this mocking behavior. Ideally we'll change this
     // to be more explicit.
     const moduleResource = moduleName && this._resolver.getModule(moduleName);
@@ -249,7 +255,7 @@ class Runtime {
       modulePath = this._resolveModule(from, moduleName);
     }
 
-    if (!this._moduleRegistry[modulePath]) {
+    if (!moduleRegistry[modulePath]) {
       // We must register the pre-allocated module object first so that any
       // circular dependencies that may arise while evaluating the module can
       // be satisfied.
@@ -257,7 +263,7 @@ class Runtime {
         filename: modulePath,
         exports: {},
       };
-      this._moduleRegistry[modulePath] = localModule;
+      moduleRegistry[modulePath] = localModule;
       if (path.extname(modulePath) === '.json') {
         localModule.exports = this._environment.global.JSON.parse(
           fs.readFileSync(modulePath, 'utf8'),
@@ -269,7 +275,7 @@ class Runtime {
         this._execModule(localModule, options);
       }
     }
-    return this._moduleRegistry[modulePath].exports;
+    return moduleRegistry[modulePath].exports;
   }
 
   requireInternalModule(from: Path, to?: string) {