diff --git a/packages/babel-core/src/transformation/file/index.js b/packages/babel-core/src/transformation/file/index.js
index 6799b2dd2d..88d5be5e84 100644
--- a/packages/babel-core/src/transformation/file/index.js
+++ b/packages/babel-core/src/transformation/file/index.js
@@ -10,7 +10,6 @@ import sourceMap from "source-map";
 import generate from "babel-generator";
 import codeFrame from "babel-code-frame";
 import traverse from "babel-traverse";
-import Logger from "./logger";
 import Store from "../../store";
 import { parse } from "babylon";
 import * as util from "../../util";
@@ -43,9 +42,7 @@ export default class File extends Store {
   constructor(opts: Object = {}) {
     super();
 
-    this.log = new Logger(this, opts.filename || "unknown");
-
-    opts = this.log.wrap(() => new OptionManager().init(opts));
+    opts = new OptionManager().init(opts);
 
     let passes = [];
     if (opts.plugins) passes.push(opts.plugins);
@@ -101,7 +98,6 @@ export default class File extends Store {
 
   pluginPasses: Array<Array<[Plugin, Object]>>;
   parserOpts: BabelParserOptions;
-  log: Logger;
   opts: Object;
   dynamicImportTypes: Object;
   dynamicImportIds: Object;
@@ -368,9 +364,9 @@ export default class File extends Store {
       }
     }
 
-    this.log.debug("Parse start");
+    util.debug(this.opts, "Parse start");
     const ast = parseCode(code, parserOpts || this.parserOpts);
-    this.log.debug("Parse stop");
+    util.debug(this.opts, "Parse stop");
     return ast;
   }
 
@@ -388,9 +384,9 @@ export default class File extends Store {
   }
 
   addAst(ast) {
-    this.log.debug("Start set AST");
+    util.debug(this.opts, "Start set AST");
     this._addAst(ast);
-    this.log.debug("End set AST");
+    util.debug(this.opts, "End set AST");
   }
 
   transform(): BabelFileResult {
@@ -405,13 +401,13 @@ export default class File extends Store {
       }
 
       this.call("pre", passes);
-      this.log.debug("Start transform traverse");
+      util.debug(this.opts, "Start transform traverse");
 
       // merge all plugin visitors into a single visitor
       const visitor = traverse.visitors.merge(visitors, passes, this.opts.wrapPluginVisitorMethod);
       traverse(this.ast, visitor, this.scope);
 
-      this.log.debug("End transform traverse");
+      util.debug(this.opts, "End transform traverse");
       this.call("post", passes);
     }
 
@@ -552,14 +548,14 @@ export default class File extends Store {
       }
     }
 
-    this.log.debug("Generation start");
+    util.debug(this.opts, "Generation start");
 
     const _result = gen(ast, opts.generatorOpts ? Object.assign(opts, opts.generatorOpts) : opts,
       this.code);
     result.code = _result.code;
     result.map = _result.map;
 
-    this.log.debug("Generation end");
+    util.debug(this.opts, "Generation end");
 
     if (this.shebang) {
       // add back shebang
diff --git a/packages/babel-core/src/transformation/file/logger.js b/packages/babel-core/src/transformation/file/logger.js
deleted file mode 100644
index 6a9503396a..0000000000
--- a/packages/babel-core/src/transformation/file/logger.js
+++ /dev/null
@@ -1,66 +0,0 @@
-import type File from "./index";
-import buildDebug from "debug";
-
-const verboseDebug = buildDebug("babel:verbose");
-const generalDebug = buildDebug("babel");
-
-const seenDeprecatedMessages = [];
-
-export default class Logger {
-  constructor(file: File, filename: string) {
-    this.filename = filename;
-    this.file = file;
-  }
-
-  filename: string;
-  file: File;
-
-  _buildMessage(msg: string): string {
-    let parts = `[BABEL] ${this.filename}`;
-    if (msg) parts += `: ${msg}`;
-    return parts;
-  }
-
-  wrap<T>(callback: () => T): T {
-    try {
-      return callback();
-    } catch (e) {
-      e.message = this._buildMessage(e.message);
-      throw e;
-    }
-  }
-
-  warn(msg: string) {
-    console.warn(this._buildMessage(msg));
-  }
-
-  error(msg: string, Constructor: typeof Error = Error): Error {
-    throw new Constructor(this._buildMessage(msg));
-  }
-
-  deprecate(msg: string) {
-    if (this.file.opts && this.file.opts.suppressDeprecationMessages) return;
-
-    msg = this._buildMessage(msg);
-
-    // already seen this message
-    if (seenDeprecatedMessages.indexOf(msg) >= 0) return;
-
-    // make sure we don't see it again
-    seenDeprecatedMessages.push(msg);
-
-    console.error(msg);
-  }
-
-  verbose(msg: string) {
-    if (verboseDebug.enabled) verboseDebug(this._buildMessage(msg));
-  }
-
-  debug(msg: string) {
-    if (generalDebug.enabled) generalDebug(this._buildMessage(msg));
-  }
-
-  deopt(node: Object, msg: string) {
-    this.debug(msg);
-  }
-}
diff --git a/packages/babel-core/src/transformation/file/options/option-manager.js b/packages/babel-core/src/transformation/file/options/option-manager.js
index 8e1f9cdf7d..0eedbe8345 100644
--- a/packages/babel-core/src/transformation/file/options/option-manager.js
+++ b/packages/babel-core/src/transformation/file/options/option-manager.js
@@ -373,8 +373,13 @@ export default class OptionManager {
   }
 
   init(opts: Object = {}): Object {
-    for (const config of buildConfigChain(opts)) {
-      this.mergeOptions(config);
+    try {
+      for (const config of buildConfigChain(opts)) {
+        this.mergeOptions(config);
+      }
+    } catch (e) {
+      e.message = util.message(opts, e.message);
+      throw e;
     }
 
     opts = this.options;
diff --git a/packages/babel-core/src/util.js b/packages/babel-core/src/util.js
index 8d3ba4142e..674f8abc5d 100644
--- a/packages/babel-core/src/util.js
+++ b/packages/babel-core/src/util.js
@@ -5,9 +5,24 @@ import includes from "lodash/includes";
 import isRegExp from "lodash/isRegExp";
 import path from "path";
 import slash from "slash";
+import buildDebug from "debug";
 
 export { inherits, inspect } from "util";
 
+const debugBabel = buildDebug("babel");
+
+export function debug(opts: Object, msg: string) {
+  debugBabel(message(opts, msg));
+}
+
+export function message(opts: Object, msg: string) {
+  // There are a few case where throws errors will try to annotate themselves multiple times, so
+  // to keep things simple we just bail out if re-wrapping the message.
+  if (/^\[BABEL\]/.test(msg)) return msg;
+
+  return `[BABEL] ${opts.filename || "unknown"}: ${msg}`;
+}
+
 /**
  * Test if a filename ends with a compilable extension.
  */
diff --git a/packages/babel-plugin-transform-react-jsx-source/src/index.js b/packages/babel-plugin-transform-react-jsx-source/src/index.js
index 1583598f22..3750d15448 100644
--- a/packages/babel-plugin-transform-react-jsx-source/src/index.js
+++ b/packages/babel-plugin-transform-react-jsx-source/src/index.js
@@ -45,9 +45,7 @@ export default function ({ types: t }) {
       }
 
       if (!state.fileNameIdentifier) {
-        const fileName = state.file.log.filename !== "unknown"
-          ? state.file.log.filename
-          : null;
+        const fileName = state.file.opts.filename;
 
         const fileNameIdentifier = path.scope.generateUidIdentifier(FILE_NAME_VAR);
         path.hub.file.scope.push({ id: fileNameIdentifier, init: t.stringLiteral(fileName) });