diff --git a/packages/babel/README.md b/packages/babel/README.md
index 110886e8a..cc5437a86 100644
--- a/packages/babel/README.md
+++ b/packages/babel/README.md
@@ -92,6 +92,21 @@ Type: `String | RegExp | Array[...String|RegExp]`<br>
 
 A [minimatch pattern](https://github.com/isaacs/minimatch), or array of patterns, which specifies the files in the build the plugin should operate on. When relying on Babel configuration files you cannot include files already excluded there.
 
+### `filter`
+
+Type: (id: string) => boolean<br>
+
+Custom [filter function](https://github.com/rollup/plugins/tree/master/packages/pluginutils#createfilter) can be used to determine whether or not certain modules should be operated upon.
+
+Usage:
+
+```js
+import { createFilter } from '@rollup/pluginutils';
+const include = 'include/**.js';
+const exclude = 'exclude/**.js';
+const filter = createFilter(include, exclude, {});
+```
+
 ### `extensions`
 
 Type: `Array[...String]`<br>
diff --git a/packages/babel/src/index.js b/packages/babel/src/index.js
index 25144027e..e631522d3 100644
--- a/packages/babel/src/index.js
+++ b/packages/babel/src/index.js
@@ -122,12 +122,14 @@ function createBabelInputPluginFactory(customCallback = returnObject) {
         let exclude;
         let include;
         let extensions;
+        let customFilter;
 
         ({
           exclude,
           extensions,
           babelHelpers,
           include,
+          filter: customFilter,
           skipPreflightCheck,
           ...babelOptions
         } = unpackInputPluginOptions(pluginOptionsWithOverrides, this.meta.rollupVersion));
@@ -135,8 +137,12 @@ function createBabelInputPluginFactory(customCallback = returnObject) {
         const extensionRegExp = new RegExp(
           `(${extensions.map(escapeRegExpCharacters).join('|')})$`
         );
-        const includeExcludeFilter = createFilter(include, exclude);
-        filter = (id) => extensionRegExp.test(stripQuery(id).bareId) && includeExcludeFilter(id);
+        if (customFilter && (include || exclude)) {
+          throw new Error('Could not handle include or exclude with custom filter together');
+        }
+        const userDefinedFilter =
+          typeof customFilter === 'function' ? customFilter : createFilter(include, exclude);
+        filter = (id) => extensionRegExp.test(stripQuery(id).bareId) && userDefinedFilter(id);
 
         return null;
       },
diff --git a/packages/babel/test/as-input-plugin.js b/packages/babel/test/as-input-plugin.js
index 32109c4ba..f6e4af33b 100644
--- a/packages/babel/test/as-input-plugin.js
+++ b/packages/babel/test/as-input-plugin.js
@@ -6,6 +6,7 @@ import { rollup } from 'rollup';
 import { SourceMapConsumer } from 'source-map';
 import jsonPlugin from '@rollup/plugin-json';
 import nodeResolvePlugin from '@rollup/plugin-node-resolve';
+import { createFilter } from '@rollup/pluginutils';
 
 import { getCode } from '../../../util/test';
 
@@ -101,6 +102,65 @@ console.log("the answer is ".concat(foo()));
   );
 });
 
+test('does not babelify excluded code with custom filter', async (t) => {
+  const filter = createFilter([], '**/foo.js');
+  const code = await generate('fixtures/exclusions/main.js', { filter });
+  // eslint-disable-next-line no-template-curly-in-string
+  t.false(code.includes('${foo()}'));
+  t.true(code.includes('=> 42'));
+  t.is(
+    code,
+    `'use strict';
+
+const foo = () => 42;
+
+console.log("the answer is ".concat(foo()));
+`
+  );
+});
+
+test('does babelify included code with custom filter', async (t) => {
+  const filter = createFilter('**/foo.js', [], {
+    resolve: __dirname
+  });
+  const code = await generate('fixtures/exclusions/main.js', { filter });
+  // eslint-disable-next-line no-template-curly-in-string
+  t.true(code.includes('${foo()}'));
+  t.false(code.includes('=> 42'));
+  t.is(
+    code,
+    `'use strict';
+
+var foo = function foo() {
+  return 42;
+};
+
+console.log(\`the answer is \${foo()}\`);
+`
+  );
+});
+
+test('can not pass include or exclude when custom filter specified', async (t) => {
+  const filter = createFilter('**/foo.js', [], {
+    resolve: __dirname
+  });
+  let errorWithExclude = '';
+  try {
+    await generate('fixtures/exclusions/main.js', { filter, exclude: [] });
+  } catch (e) {
+    errorWithExclude = e.message;
+  }
+  t.true(!!errorWithExclude);
+
+  let errorWithInclude = '';
+  try {
+    await generate('fixtures/exclusions/main.js', { filter, include: [] });
+  } catch (e) {
+    errorWithInclude = e.message;
+  }
+  t.true(!!errorWithInclude);
+});
+
 test('generates sourcemap by default', async (t) => {
   const bundle = await rollup({
     input: 'fixtures/class/main.js',
diff --git a/packages/babel/types/index.d.ts b/packages/babel/types/index.d.ts
index 52c9558be..3ba0195f4 100644
--- a/packages/babel/types/index.d.ts
+++ b/packages/babel/types/index.d.ts
@@ -1,5 +1,5 @@
 import { Plugin, PluginContext, TransformPluginContext } from 'rollup';
-import { FilterPattern } from '@rollup/pluginutils';
+import { FilterPattern, CreateFilter } from '@rollup/pluginutils';
 import * as babelCore from '@babel/core';
 
 export interface RollupBabelInputPluginOptions
@@ -14,6 +14,16 @@ export interface RollupBabelInputPluginOptions
    * @default undefined;
    */
   exclude?: FilterPattern;
+  /**
+   * Custom filter function can be used to determine whether or not certain modules should be operated upon.
+   * Example:
+   *   import { createFilter } from '@rollup/pluginutils';
+   *   const include = 'include/**.js';
+   *   const exclude = 'exclude/**.js';
+   *   const filter = createFilter(include, exclude, {});
+   * @default undefined;
+   */
+  filter?: ReturnType<CreateFilter>;
   /**
    * An array of file extensions that Babel should transpile. If you want to transpile TypeScript files with this plugin it's essential to include .ts and .tsx in this option.
    * @default ['.js', '.jsx', '.es6', '.es', '.mjs']