diff --git a/packages/babel-core/src/config/build-config-chain.js b/packages/babel-core/src/config/build-config-chain.js
index d52a75666c..56995ea6f2 100644
--- a/packages/babel-core/src/config/build-config-chain.js
+++ b/packages/babel-core/src/config/build-config-chain.js
@@ -7,7 +7,9 @@ import buildDebug from "debug";
 
 const debug = buildDebug("babel:config:config-chain");
 
-import { findConfigs, loadConfig } from "./loading/files";
+import { findConfigs, loadConfig, type ConfigFile } from "./loading/files";
+
+import { makeWeakCache, makeStrongCache } from "./caching";
 
 type ConfigItem = {
   type: "options" | "arguments",
@@ -17,25 +19,32 @@ type ConfigItem = {
   loc: string,
 };
 
+type ConfigRaw = {
+  type: "options" | "arguments",
+  options: {},
+  alias: string,
+  dirname: string,
+};
+
 export default function buildConfigChain(opts: {}): Array<ConfigItem> | null {
   if (typeof opts.filename !== "string" && opts.filename != null) {
     throw new Error(".filename must be a string, null, or undefined");
   }
 
   const filename = opts.filename ? path.resolve(opts.filename) : null;
-  const builder = new ConfigChainBuilder(filename);
+  const builder = new ConfigChainBuilder(
+    filename ? new LoadedFile(filename) : null,
+  );
 
+  const envKey = getEnv();
   try {
-    builder.mergeConfig({
-      type: "arguments",
-      options: opts,
-      alias: "base",
-      dirname: process.cwd(),
-    });
+    builder.mergeConfigArguments(opts, process.cwd(), envKey);
 
     // resolve all .babelrc files
     if (opts.babelrc !== false && filename) {
-      builder.findConfigs(filename);
+      findConfigs(path.dirname(filename)).forEach(configFile =>
+        builder.mergeConfigFile(configFile, envKey),
+      );
     }
   } catch (e) {
     if (e.code !== "BABEL_IGNORED_FILE") throw e;
@@ -47,30 +56,346 @@ export default function buildConfigChain(opts: {}): Array<ConfigItem> | null {
 }
 
 class ConfigChainBuilder {
-  filename: string | null;
-  configs: Array<ConfigItem>;
-  possibleDirs: null | Array<string>;
+  file: LoadedFile | null;
+  configs: Array<ConfigItem> = [];
+
+  constructor(file: LoadedFile | null) {
+    this.file = file;
+  }
+
+  mergeConfigArguments(opts: {}, dirname: string, envKey: string) {
+    flattenArgumentsOptionsParts(opts, dirname, envKey).forEach(part =>
+      this._processConfigPart(part, envKey),
+    );
+  }
+
+  mergeConfigFile(file: ConfigFile, envKey: string) {
+    flattenFileOptionsParts(file)(envKey).forEach(part =>
+      this._processConfigPart(part, envKey),
+    );
+  }
+
+  _processConfigPart(part: ConfigPart, envKey: string) {
+    if (part.part === "config") {
+      const { ignore, only } = part;
+
+      // Bail out ASAP if this file is ignored so that we run as little logic as possible on ignored files.
+      if (
+        this.file &&
+        this.file.shouldIgnore(ignore, only, part.config.dirname)
+      ) {
+        // TODO(logan): This is a really gross way to bail out. Avoid this in rewrite.
+        throw Object.assign((new Error("This file has been ignored."): any), {
+          code: "BABEL_IGNORED_FILE",
+        });
+      }
+
+      this.configs.push(part.config);
+    } else {
+      const extendsConfig = loadConfig(part.path, part.dirname);
+
+      const existingConfig = this.configs.some(config => {
+        return config.alias === extendsConfig.filepath;
+      });
+      if (!existingConfig) {
+        this.mergeConfigFile(extendsConfig, envKey);
+      }
+    }
+  }
+}
+
+/**
+ * Given the root config object passed to Babel, split it into the separate
+ * config parts. The resulting config objects in the 'ConfigPart' have their
+ * object identity preserved between calls so that they can be used for caching.
+ */
+function flattenArgumentsOptionsParts(
+  opts: {},
+  dirname: string,
+  envKey: string,
+): Array<ConfigPart> {
+  const raw = [];
+
+  const env = typeof opts.env === "object" ? opts.env : null;
+  const plugins = Array.isArray(opts.plugins) ? opts.plugins : null;
+  const presets = Array.isArray(opts.presets) ? opts.presets : null;
+  const passPerPreset =
+    typeof opts.passPerPreset === "boolean" ? opts.passPerPreset : false;
+
+  if (env) {
+    raw.push(...flattenArgumentsEnvOptionsParts(env)(dirname)(envKey));
+  }
+
+  const innerOpts = Object.assign({}, opts);
+  // If the env, plugins, and presets values on the object aren't arrays or
+  // objects, leave them in the base opts so that normal options validation
+  // will throw errors on them later.
+  if (env) delete innerOpts.env;
+  if (plugins) delete innerOpts.plugins;
+  if (presets) {
+    delete innerOpts.presets;
+    delete innerOpts.passPerPreset;
+  }
+  delete innerOpts.extends;
+
+  if (Object.keys(innerOpts).length > 0) {
+    raw.push(
+      ...flattenOptionsParts({
+        type: "arguments",
+        options: innerOpts,
+        alias: "base",
+        dirname,
+      }),
+    );
+  }
+
+  if (plugins) {
+    raw.push(...flattenArgumentsPluginsOptionsParts(plugins)(dirname));
+  }
+  if (presets) {
+    raw.push(
+      ...flattenArgumentsPresetsOptionsParts(presets)(passPerPreset)(dirname),
+    );
+  }
+
+  if (opts.extends != null) {
+    raw.push(
+      ...flattenOptionsParts(
+        buildArgumentsRawConfig({ extends: opts.extends }, dirname),
+      ),
+    );
+  }
+
+  return raw;
+}
+
+/**
+ * For the top-level 'options' object, we cache the env list based on
+ * the object identity of the 'env' object.
+ */
+const flattenArgumentsEnvOptionsParts = makeWeakCache((env: {}) => {
+  const options = { env };
+
+  return makeStrongCache((dirname: string) =>
+    flattenOptionsPartsLookup(buildArgumentsRawConfig(options, dirname)),
+  );
+});
+
+/**
+ * For the top-level 'options' object, we cache the plugin list based on
+ * the object identity of the 'plugins' object.
+ */
+const flattenArgumentsPluginsOptionsParts = makeWeakCache(
+  (plugins: Array<mixed>) => {
+    const options = { plugins };
+
+    return makeStrongCache((dirname: string) =>
+      flattenOptionsParts(buildArgumentsRawConfig(options, dirname)),
+    );
+  },
+);
+
+/**
+ * For the top-level 'options' object, we cache the preset list based on
+ * the object identity of the 'presets' object.
+ */
+const flattenArgumentsPresetsOptionsParts = makeWeakCache(
+  (presets: Array<mixed>) =>
+    makeStrongCache((passPerPreset: ?boolean) => {
+      // The concept of passPerPreset is integrally tied to the preset list
+      // so unfortunately we need to copy both values here, adding an extra
+      // layer of caching functions.
+      const options = { presets, passPerPreset };
+
+      return makeStrongCache((dirname: string) =>
+        flattenOptionsParts(buildArgumentsRawConfig(options, dirname)),
+      );
+    }),
+);
+
+function buildArgumentsRawConfig(options: {}, dirname: string): ConfigRaw {
+  return {
+    type: "arguments",
+    options,
+    alias: "base",
+    dirname,
+  };
+}
+
+/**
+ * Given a config from a specific file, return a list of ConfigPart objects
+ * with object identity preserved for all 'config' part objects for use
+ * with caching later in config processing.
+ */
+const flattenFileOptionsParts = makeWeakCache((file: ConfigFile) => {
+  return flattenOptionsPartsLookup({
+    type: "options",
+    options: file.options,
+    alias: file.filepath,
+    dirname: file.dirname,
+  });
+});
+
+/**
+ * Given a config, create a function that will return the config parts for
+ * the environment passed as the first argument.
+ */
+function flattenOptionsPartsLookup(
+  config: ConfigRaw,
+): (string | null) => Array<ConfigPart> {
+  const parts = flattenOptionsParts(config);
+
+  const def = parts.filter(part => part.activeEnv === null);
+  const lookup = new Map();
+
+  parts.forEach(part => {
+    if (part.activeEnv !== null) lookup.set(part.activeEnv, []);
+  });
+
+  for (const [activeEnv, values] of lookup) {
+    parts.forEach(part => {
+      if (part.activeEnv === null || part.activeEnv === activeEnv) {
+        values.push(part);
+      }
+    });
+  }
+
+  return envKey => lookup.get(envKey) || def;
+}
+
+type ConfigPart =
+  | {
+      part: "config",
+      config: ConfigItem,
+      ignore: ?Array<mixed>,
+      only: ?Array<mixed>,
+      activeEnv: string | null,
+    }
+  | {
+      part: "extends",
+      path: string,
+      dirname: string,
+      activeEnv: string | null,
+    };
+
+/**
+ * Given a generic config object, flatten it into its various parts so that
+ * then can be cached and processed later.
+ */
+function flattenOptionsParts(
+  rawConfig: ConfigRaw,
+  activeEnv: string | null = null,
+): Array<ConfigPart> {
+  const { type, options: rawOpts, alias, dirname } = rawConfig;
+
+  if (rawOpts.ignore != null && !Array.isArray(rawOpts.ignore)) {
+    throw new Error(
+      `.ignore should be an array, ${JSON.stringify(rawOpts.ignore)} given`,
+    );
+  }
+  if (rawOpts.only != null && !Array.isArray(rawOpts.only)) {
+    throw new Error(
+      `.only should be an array, ${JSON.stringify(rawOpts.only)} given`,
+    );
+  }
+  const ignore = rawOpts.ignore || null;
+  const only = rawOpts.only || null;
+
+  const parts = [];
+
+  if (
+    rawOpts.env != null &&
+    (typeof rawOpts.env !== "object" || Array.isArray(rawOpts.env))
+  ) {
+    throw new Error(".env block must be an object, null, or undefined");
+  }
+
+  const rawEnv = rawOpts.env || {};
+
+  Object.keys(rawEnv).forEach(envKey => {
+    const envOpts = rawEnv[envKey];
+
+    if (envOpts !== undefined && activeEnv !== null && activeEnv !== envKey) {
+      throw new Error(`Unreachable .env[${envKey}] block detected`);
+    }
+
+    if (
+      envOpts != null &&
+      (typeof envOpts !== "object" || Array.isArray(envOpts))
+    ) {
+      throw new Error(".env[...] block must be an object, null, or undefined");
+    }
+
+    if (envOpts) {
+      parts.push(
+        ...flattenOptionsParts(
+          {
+            type,
+            options: envOpts,
+            alias: alias + `.env.${envKey}`,
+            dirname,
+          },
+          envKey,
+        ),
+      );
+    }
+  });
+
+  const options = Object.assign({}, rawOpts);
+  delete options.env;
+  delete options.extends;
+
+  parts.push({
+    part: "config",
+    config: {
+      type,
+      options,
+      alias,
+      loc: alias,
+      dirname,
+    },
+    ignore,
+    only,
+    activeEnv,
+  });
+
+  if (rawOpts.extends != null) {
+    if (typeof rawOpts.extends !== "string") {
+      throw new Error(".extends must be a string");
+    }
+
+    parts.push({
+      part: "extends",
+      path: rawOpts.extends,
+      dirname,
+      activeEnv,
+    });
+  }
+
+  return parts;
+}
+
+/**
+ * Track a given file and expose function to check if it should be ignored.
+ */
+class LoadedFile {
+  filename: string;
+  possibleDirs: null | Array<string> = null;
 
   constructor(filename) {
-    this.configs = [];
     this.filename = filename;
-    this.possibleDirs = null;
   }
 
   /**
    * Tests if a filename should be ignored based on "ignore" and "only" options.
    */
-  shouldIgnore(ignore: mixed, only: mixed, dirname: string): boolean {
-    if (!this.filename) return false;
-
+  shouldIgnore(
+    ignore: ?Array<mixed>,
+    only: ?Array<mixed>,
+    dirname: string,
+  ): boolean {
     if (ignore) {
-      if (!Array.isArray(ignore)) {
-        throw new Error(
-          `.ignore should be an array, ${JSON.stringify(ignore)} given`,
-        );
-      }
-
-      if (this.matchesPatterns(ignore, dirname)) {
+      if (this._matchesPatterns(ignore, dirname)) {
         debug(
           "Ignored %o because it matched one of %O from %o",
           this.filename,
@@ -82,13 +407,7 @@ class ConfigChainBuilder {
     }
 
     if (only) {
-      if (!Array.isArray(only)) {
-        throw new Error(
-          `.only should be an array, ${JSON.stringify(only)} given`,
-        );
-      }
-
-      if (!this.matchesPatterns(only, dirname)) {
+      if (!this._matchesPatterns(only, dirname)) {
         debug(
           "Ignored %o because it failed to match one of %O from %o",
           this.filename,
@@ -106,12 +425,7 @@ class ConfigChainBuilder {
    * Returns result of calling function with filename if pattern is a function.
    * Otherwise returns result of matching pattern Regex with filename.
    */
-  matchesPatterns(patterns: Array<mixed>, dirname: string) {
-    const filename = this.filename;
-    if (!filename) {
-      throw new Error("Assertion failure: .filename should always exist here");
-    }
-
+  _matchesPatterns(patterns: Array<mixed>, dirname: string): boolean {
     const res = [];
     const strings = [];
     const fns = [];
@@ -127,6 +441,7 @@ class ConfigChainBuilder {
       }
     });
 
+    const filename = this.filename;
     if (res.some(re => re.test(filename))) return true;
     if (fns.some(fn => fn(filename))) return true;
 
@@ -165,87 +480,4 @@ class ConfigChainBuilder {
 
     return false;
   }
-
-  findConfigs(loc: string) {
-    findConfigs(path.dirname(loc)).forEach(({ filepath, dirname, options }) => {
-      this.mergeConfig({
-        type: "options",
-        options,
-        alias: filepath,
-        dirname,
-      });
-    });
-  }
-
-  mergeConfig({ type, options: rawOpts, alias, dirname }) {
-    // Bail out ASAP if this file is ignored so that we run as little logic as possible on ignored files.
-    if (
-      this.filename &&
-      this.shouldIgnore(rawOpts.ignore || null, rawOpts.only || null, dirname)
-    ) {
-      // TODO(logan): This is a really cross way to bail out. Avoid this in rewrite.
-      throw Object.assign((new Error("This file has been ignored."): any), {
-        code: "BABEL_IGNORED_FILE",
-      });
-    }
-
-    const options = Object.assign({}, rawOpts);
-    delete options.env;
-    delete options.extends;
-
-    const envKey = getEnv();
-
-    if (
-      rawOpts.env != null &&
-      (typeof rawOpts.env !== "object" || Array.isArray(rawOpts.env))
-    ) {
-      throw new Error(".env block must be an object, null, or undefined");
-    }
-
-    const envOpts = rawOpts.env && rawOpts.env[envKey];
-
-    if (
-      envOpts != null &&
-      (typeof envOpts !== "object" || Array.isArray(envOpts))
-    ) {
-      throw new Error(".env[...] block must be an object, null, or undefined");
-    }
-
-    if (envOpts) {
-      this.mergeConfig({
-        type,
-        options: envOpts,
-        alias: `${alias}.env.${envKey}`,
-        dirname: dirname,
-      });
-    }
-
-    this.configs.push({
-      type,
-      options,
-      alias,
-      loc: alias,
-      dirname,
-    });
-
-    if (rawOpts.extends) {
-      if (typeof rawOpts.extends !== "string") {
-        throw new Error(".extends must be a string");
-      }
-
-      const extendsConfig = loadConfig(rawOpts.extends, dirname);
-
-      const existingConfig = this.configs.some(config => {
-        return config.alias === extendsConfig.filepath;
-      });
-      if (!existingConfig) {
-        this.mergeConfig({
-          type: "options",
-          alias: extendsConfig.filepath,
-          options: extendsConfig.options,
-          dirname: extendsConfig.dirname,
-        });
-      }
-    }
-  }
 }
diff --git a/packages/babel-core/src/config/caching.js b/packages/babel-core/src/config/caching.js
index 24d3e748bb..052e2803c3 100644
--- a/packages/babel-core/src/config/caching.js
+++ b/packages/babel-core/src/config/caching.js
@@ -31,7 +31,7 @@ export function makeStrongCache<ArgT, ResultT>(
  * configures its caching behavior. Cached values are stored weakly and the function argument must be
  * an object type.
  */
-export function makeWeakCache<ArgT: {}, ResultT>(
+export function makeWeakCache<ArgT: {} | Array<*>, ResultT>(
   handler: (ArgT, CacheConfigurator) => ResultT,
   autoPermacache?: boolean,
 ): ArgT => ResultT {
diff --git a/packages/babel-core/src/config/loading/files/configuration.js b/packages/babel-core/src/config/loading/files/configuration.js
index 861ab73039..09bd840230 100644
--- a/packages/babel-core/src/config/loading/files/configuration.js
+++ b/packages/babel-core/src/config/loading/files/configuration.js
@@ -10,7 +10,7 @@ import { makeStrongCache } from "../../caching";
 
 const debug = buildDebug("babel:config:loading:files:configuration");
 
-type ConfigFile = {
+export type ConfigFile = {
   filepath: string,
   dirname: string,
   options: {},
diff --git a/packages/babel-core/src/config/loading/files/index-browser.js b/packages/babel-core/src/config/loading/files/index-browser.js
index 79d5325291..2c8f80d79f 100644
--- a/packages/babel-core/src/config/loading/files/index-browser.js
+++ b/packages/babel-core/src/config/loading/files/index-browser.js
@@ -1,6 +1,6 @@
 // @flow
 
-type ConfigFile = {
+export type ConfigFile = {
   filepath: string,
   dirname: string,
   options: {},
diff --git a/packages/babel-core/test/config-chain.js b/packages/babel-core/test/config-chain.js
index 3f93a7d18c..aeee3c7cad 100644
--- a/packages/babel-core/test/config-chain.js
+++ b/packages/babel-core/test/config-chain.js
@@ -1,4 +1,5 @@
 import assert from "assert";
+import fs from "fs";
 import path from "path";
 import buildConfigChain from "../lib/config/build-config-chain";
 
@@ -52,6 +53,234 @@ describe("buildConfigChain", function() {
     });
   });
 
+  describe("caching", function() {
+    describe("programmatic options", function() {
+      it("should not cache the input options by identity", () => {
+        const comments = false;
+
+        const chain1 = buildConfigChain({ comments });
+        const chain2 = buildConfigChain({ comments });
+
+        assert.equal(chain1.length, 1);
+        assert.equal(chain2.length, 1);
+        assert.notStrictEqual(chain1[0], chain2[0]);
+      });
+
+      it("should cache the env options by identity", () => {
+        process.env.NODE_ENV = "foo";
+        const env = {
+          foo: {
+            comments: false,
+          },
+        };
+
+        const chain1 = buildConfigChain({ env });
+        const chain2 = buildConfigChain({ env });
+
+        assert.equal(chain1.length, 2);
+        assert.equal(chain2.length, 2);
+        assert.strictEqual(chain1[0], chain2[0]);
+        assert.strictEqual(chain1[1], chain2[1]);
+      });
+
+      it("should cache the plugin options by identity", () => {
+        const plugins = [];
+
+        const chain1 = buildConfigChain({ plugins });
+        const chain2 = buildConfigChain({ plugins });
+
+        assert.equal(chain1.length, 1);
+        assert.equal(chain2.length, 1);
+        assert.strictEqual(chain1[0], chain2[0]);
+      });
+
+      it("should cache the presets options by identity", () => {
+        const presets = [];
+
+        const chain1 = buildConfigChain({ presets });
+        const chain2 = buildConfigChain({ presets });
+
+        assert.equal(chain1.length, 1);
+        assert.equal(chain2.length, 1);
+        assert.strictEqual(chain1[0], chain2[0]);
+      });
+
+      it("should not cache the presets options with passPerPreset", () => {
+        const presets = [];
+
+        const chain1 = buildConfigChain({ presets });
+        const chain2 = buildConfigChain({ presets, passPerPreset: true });
+        const chain3 = buildConfigChain({ presets, passPerPreset: false });
+
+        assert.equal(chain1.length, 1);
+        assert.equal(chain2.length, 1);
+        assert.equal(chain3.length, 1);
+        assert.notStrictEqual(chain1[0], chain2[0]);
+        assert.strictEqual(chain1[0], chain3[0]);
+        assert.notStrictEqual(chain2[0], chain3[0]);
+      });
+    });
+
+    describe("config file options", function() {
+      function touch(filepath) {
+        const s = fs.statSync(filepath);
+        fs.utimesSync(
+          filepath,
+          s.atime,
+          s.mtime + Math.random() > 0.5 ? 1 : -1,
+        );
+      }
+
+      it("should cache package.json files by mtime", () => {
+        const filename = fixture(
+          "complex-plugin-config",
+          "config-identity",
+          "pkg",
+          "src.js",
+        );
+        const pkgJSON = fixture(
+          "complex-plugin-config",
+          "config-identity",
+          "pkg",
+          "package.json",
+        );
+
+        const chain1 = buildConfigChain({ filename });
+        const chain2 = buildConfigChain({ filename });
+
+        touch(pkgJSON);
+
+        const chain3 = buildConfigChain({ filename });
+        const chain4 = buildConfigChain({ filename });
+
+        assert.equal(chain1.length, 3);
+        assert.equal(chain2.length, 3);
+        assert.equal(chain3.length, 3);
+        assert.equal(chain4.length, 3);
+        assert.equal(chain1[1].alias, pkgJSON);
+        assert.equal(chain2[1].alias, pkgJSON);
+        assert.equal(chain3[1].alias, pkgJSON);
+        assert.equal(chain4[1].alias, pkgJSON);
+        assert.strictEqual(chain1[1], chain2[1]);
+
+        // Identity changed after touch().
+        assert.notStrictEqual(chain3[1], chain1[1]);
+        assert.strictEqual(chain3[1], chain4[1]);
+      });
+
+      it("should cache .babelrc files by mtime", () => {
+        const filename = fixture(
+          "complex-plugin-config",
+          "config-identity",
+          "babelrc",
+          "src.js",
+        );
+        const babelrcFile = fixture(
+          "complex-plugin-config",
+          "config-identity",
+          "babelrc",
+          ".babelrc",
+        );
+
+        const chain1 = buildConfigChain({ filename });
+        const chain2 = buildConfigChain({ filename });
+
+        touch(babelrcFile);
+
+        const chain3 = buildConfigChain({ filename });
+        const chain4 = buildConfigChain({ filename });
+
+        assert.equal(chain1.length, 3);
+        assert.equal(chain2.length, 3);
+        assert.equal(chain3.length, 3);
+        assert.equal(chain4.length, 3);
+        assert.equal(chain1[1].alias, babelrcFile);
+        assert.equal(chain2[1].alias, babelrcFile);
+        assert.equal(chain3[1].alias, babelrcFile);
+        assert.equal(chain4[1].alias, babelrcFile);
+        assert.strictEqual(chain1[1], chain2[1]);
+
+        // Identity changed after touch().
+        assert.notStrictEqual(chain3[1], chain1[1]);
+        assert.strictEqual(chain3[1], chain4[1]);
+      });
+
+      it("should cache .babelignore files by mtime", () => {
+        const filename = fixture(
+          "complex-plugin-config",
+          "config-identity",
+          "babelignore",
+          "src.js",
+        );
+        const babelignoreFile = fixture(
+          "complex-plugin-config",
+          "config-identity",
+          "babelignore",
+          ".babelignore",
+        );
+
+        const chain1 = buildConfigChain({ filename });
+        const chain2 = buildConfigChain({ filename });
+
+        touch(babelignoreFile);
+
+        const chain3 = buildConfigChain({ filename });
+        const chain4 = buildConfigChain({ filename });
+
+        assert.equal(chain1.length, 6);
+        assert.equal(chain2.length, 6);
+        assert.equal(chain3.length, 6);
+        assert.equal(chain4.length, 6);
+        assert.equal(chain1[4].alias, babelignoreFile);
+        assert.equal(chain2[4].alias, babelignoreFile);
+        assert.equal(chain3[4].alias, babelignoreFile);
+        assert.equal(chain4[4].alias, babelignoreFile);
+        assert.strictEqual(chain1[4], chain2[4]);
+
+        // Identity changed after touch().
+        assert.notStrictEqual(chain3[4], chain1[4]);
+        assert.strictEqual(chain3[4], chain4[4]);
+      });
+
+      it("should cache .babelrc.js files programmable behavior", () => {
+        const filename = fixture(
+          "complex-plugin-config",
+          "config-identity",
+          "babelrc-js",
+          "src.js",
+        );
+        const babelrcFile = fixture(
+          "complex-plugin-config",
+          "config-identity",
+          "babelrc-js",
+          ".babelrc.js",
+        );
+
+        const chain1 = buildConfigChain({ filename });
+        const chain2 = buildConfigChain({ filename });
+
+        process.env.NODE_ENV = "new-env";
+
+        const chain3 = buildConfigChain({ filename });
+        const chain4 = buildConfigChain({ filename });
+
+        assert.equal(chain1.length, 3);
+        assert.equal(chain2.length, 3);
+        assert.equal(chain3.length, 3);
+        assert.equal(chain4.length, 3);
+        assert.equal(chain1[1].alias, babelrcFile);
+        assert.equal(chain2[1].alias, babelrcFile);
+        assert.equal(chain3[1].alias, babelrcFile);
+        assert.equal(chain4[1].alias, babelrcFile);
+        assert.strictEqual(chain1[1], chain2[1]);
+
+        // Identity changed after changing the NODE_ENV.
+        assert.notStrictEqual(chain3[1], chain1[1]);
+        assert.strictEqual(chain3[1], chain4[1]);
+      });
+    });
+  });
+
   it("dir1", function() {
     const chain = buildConfigChain({
       filename: fixture("dir1", "src.js"),
diff --git a/packages/babel-core/test/fixtures/config/complex-plugin-config/config-identity/babelignore/.babelignore b/packages/babel-core/test/fixtures/config/complex-plugin-config/config-identity/babelignore/.babelignore
new file mode 100644
index 0000000000..3f6555f66d
--- /dev/null
+++ b/packages/babel-core/test/fixtures/config/complex-plugin-config/config-identity/babelignore/.babelignore
@@ -0,0 +1 @@
+fake-file.js
diff --git a/packages/babel-core/test/fixtures/config/complex-plugin-config/config-identity/babelrc-js/.babelrc.js b/packages/babel-core/test/fixtures/config/complex-plugin-config/config-identity/babelrc-js/.babelrc.js
new file mode 100644
index 0000000000..968dcc5d7d
--- /dev/null
+++ b/packages/babel-core/test/fixtures/config/complex-plugin-config/config-identity/babelrc-js/.babelrc.js
@@ -0,0 +1,7 @@
+module.exports = function(api) {
+  api.env();
+
+  return {
+    comments: false,
+  };
+}
diff --git a/packages/babel-core/test/fixtures/config/complex-plugin-config/config-identity/babelrc/.babelrc b/packages/babel-core/test/fixtures/config/complex-plugin-config/config-identity/babelrc/.babelrc
new file mode 100644
index 0000000000..68628f8709
--- /dev/null
+++ b/packages/babel-core/test/fixtures/config/complex-plugin-config/config-identity/babelrc/.babelrc
@@ -0,0 +1,3 @@
+{
+  comments: false,
+}
diff --git a/packages/babel-core/test/fixtures/config/complex-plugin-config/config-identity/pkg/package.json b/packages/babel-core/test/fixtures/config/complex-plugin-config/config-identity/pkg/package.json
new file mode 100644
index 0000000000..612c17bb1f
--- /dev/null
+++ b/packages/babel-core/test/fixtures/config/complex-plugin-config/config-identity/pkg/package.json
@@ -0,0 +1,5 @@
+{
+  "babel": {
+    "comments": false
+  }
+}