diff --git a/packages/babel-jest/src/index.js b/packages/babel-jest/src/index.js
index 331bc793e76f..3751e146f08b 100644
--- a/packages/babel-jest/src/index.js
+++ b/packages/babel-jest/src/index.js
@@ -9,7 +9,7 @@
  */
 
 import type {Path, ProjectConfig} from 'types/Config';
-import type {TransformOptions} from 'types/Transform';
+import type {CacheKeyOptions, TransformOptions} from 'types/Transform';
 
 import crypto from 'crypto';
 import fs from 'fs';
@@ -82,7 +82,7 @@ const createTransformer = (options: any) => {
       fileData: string,
       filename: Path,
       configString: string,
-      {instrument}: TransformOptions,
+      {instrument, rootDir}: CacheKeyOptions,
     ): string {
       return crypto
         .createHash('md5')
@@ -90,7 +90,7 @@ const createTransformer = (options: any) => {
         .update('\0', 'utf8')
         .update(fileData)
         .update('\0', 'utf8')
-        .update(filename)
+        .update(path.relative(rootDir, filename))
         .update('\0', 'utf8')
         .update(configString)
         .update('\0', 'utf8')
diff --git a/packages/jest-runtime/src/script_transformer.js b/packages/jest-runtime/src/script_transformer.js
index a459e7c6e10c..df25c07a1956 100644
--- a/packages/jest-runtime/src/script_transformer.js
+++ b/packages/jest-runtime/src/script_transformer.js
@@ -77,6 +77,7 @@ class ScriptTransformer {
           transformer.getCacheKey(fileData, filename, configString, {
             instrument,
             mapCoverage,
+            rootDir: this._config.rootDir,
           }),
         )
         .update(CACHE_VERSION)
diff --git a/types/Transform.js b/types/Transform.js
index bdb04d1ae555..576720069956 100644
--- a/types/Transform.js
+++ b/types/Transform.js
@@ -28,6 +28,7 @@ export type TransformOptions = {|
 export type CacheKeyOptions = {|
   instrument: boolean,
   mapCoverage: boolean,
+  rootDir: string,
 |};
 
 export type Transformer = {|