diff --git a/packages/babel-core/src/transform-file-sync.js b/packages/babel-core/src/transform-file-sync.js
index 496c26f888..28b89e05c9 100644
--- a/packages/babel-core/src/transform-file-sync.js
+++ b/packages/babel-core/src/transform-file-sync.js
@@ -8,13 +8,14 @@ export default function transformFileSync(
   filename: string,
   opts: ?InputOptions,
 ): FileResult | null {
+  let options;
   if (opts == null) {
-    opts = { filename };
+    options = { filename };
   } else if (opts && typeof opts === "object") {
-    opts = Object.assign(opts, { filename });
+    options = Object.assign({}, opts, { filename });
   }
 
-  const config = loadConfig(opts);
+  const config = loadConfig(options);
   if (config === null) return null;
 
   return runSync(config, fs.readFileSync(filename, "utf8"));
diff --git a/packages/babel-core/src/transform-file.js b/packages/babel-core/src/transform-file.js
index 0c884f2918..e73b855c0c 100644
--- a/packages/babel-core/src/transform-file.js
+++ b/packages/babel-core/src/transform-file.js
@@ -10,21 +10,22 @@ type TransformFile = {
 };
 
 export default ((function transformFile(filename, opts, callback) {
+  let options;
   if (typeof opts === "function") {
     callback = opts;
     opts = undefined;
   }
 
   if (opts == null) {
-    opts = { filename };
+    options = { filename };
   } else if (opts && typeof opts === "object") {
-    opts = Object.assign(opts, { filename });
+    options = Object.assign({}, opts, { filename });
   }
 
   process.nextTick(() => {
     let cfg;
     try {
-      cfg = loadConfig(opts);
+      cfg = loadConfig(options);
       if (cfg === null) return callback(null, null);
     } catch (err) {
       return callback(err);
diff --git a/packages/babel-core/test/api.js b/packages/babel-core/test/api.js
index 215a8960f1..dfbe5a8504 100644
--- a/packages/babel-core/test/api.js
+++ b/packages/babel-core/test/api.js
@@ -118,26 +118,33 @@ describe("api", function() {
   });
 
   it("transformFile", function(done) {
-    babel.transformFile(
-      __dirname + "/fixtures/api/file.js",
-      {
-        babelrc: false,
-      },
-      function(err, res) {
-        if (err) return done(err);
-        assert.equal(res.code, "foo();");
-        done();
-      },
-    );
+    const options = {
+      babelrc: false,
+    };
+    Object.freeze(options);
+    babel.transformFile(__dirname + "/fixtures/api/file.js", options, function(
+      err,
+      res,
+    ) {
+      if (err) return done(err);
+      assert.equal(res.code, "foo();");
+      // keep user options untouched
+      assert.deepEqual(options, { babelrc: false });
+      done();
+    });
   });
 
   it("transformFileSync", function() {
+    const options = {
+      babelrc: false,
+    };
+    Object.freeze(options);
     assert.equal(
-      babel.transformFileSync(__dirname + "/fixtures/api/file.js", {
-        babelrc: false,
-      }).code,
+      babel.transformFileSync(__dirname + "/fixtures/api/file.js", options)
+        .code,
       "foo();",
     );
+    assert.deepEqual(options, { babelrc: false });
   });
 
   it("options throw on falsy true", function() {