diff --git a/protobuf.bzl b/protobuf.bzl
index 3998e77b03..41a46f754e 100644
--- a/protobuf.bzl
+++ b/protobuf.bzl
@@ -4,7 +4,24 @@ def _GetPath(ctx, path):
   else:
     return path
 
+def _IsNewExternal(ctx):
+  # Bazel 0.4.4 and older have genfiles paths that look like:
+  #   bazel-out/local-fastbuild/genfiles/external/repo/foo
+  # After the exec root rearrangement, they look like:
+  #   ../repo/bazel-out/local-fastbuild/genfiles/foo
+  return ctx.label.workspace_root.startswith("../")
+
 def _GenDir(ctx):
+  if _IsNewExternal(ctx):
+    # We are using the fact that Bazel 0.4.4+ provides repository-relative paths
+    # for ctx.genfiles_dir.
+    return ctx.genfiles_dir.path + (
+        "/" + ctx.attr.includes[0] if ctx.attr.includes and ctx.attr.includes[0] else "")
+  # This means that we're either in the old version OR the new version in the local repo.
+  # Either way, appending the source path to the genfiles dir works.
+  return ctx.var["GENDIR"] + "/" + _SourceDir(ctx)
+
+def _SourceDir(ctx):
   if not ctx.attr.includes:
     return ctx.label.workspace_root
   if not ctx.attr.includes[0]:
@@ -51,9 +68,10 @@ def _proto_gen_impl(ctx):
   srcs = ctx.files.srcs
   deps = []
   deps += ctx.files.srcs
+  source_dir = _SourceDir(ctx)
   gen_dir = _GenDir(ctx)
-  if gen_dir:
-    import_flags = ["-I" + gen_dir, "-I" + ctx.var["GENDIR"] + "/" + gen_dir]
+  if source_dir:
+    import_flags = ["-I" + source_dir, "-I" + gen_dir]
   else:
     import_flags = ["-I."]
 
@@ -63,9 +81,9 @@ def _proto_gen_impl(ctx):
 
   args = []
   if ctx.attr.gen_cc:
-    args += ["--cpp_out=" + ctx.var["GENDIR"] + "/" + gen_dir]
+    args += ["--cpp_out=" + gen_dir]
   if ctx.attr.gen_py:
-    args += ["--python_out=" + ctx.var["GENDIR"] + "/" + gen_dir]
+    args += ["--python_out=" + gen_dir]
 
   inputs = srcs + deps
   if ctx.executable.plugin:
@@ -76,7 +94,7 @@ def _proto_gen_impl(ctx):
     if not lang:
       fail("cannot infer the target language of plugin", "plugin_language")
 
-    outdir = ctx.var["GENDIR"] + "/" + gen_dir
+    outdir = gen_dir
     if ctx.attr.plugin_options:
       outdir = ",".join(ctx.attr.plugin_options) + ":" + outdir
     args += ["--plugin=protoc-gen-%s=%s" % (lang, plugin.path)]
@@ -141,7 +159,7 @@ Args:
     compiler.
   plugin_language: the language of the generated sources
   plugin_options: a list of options to be passed to the plugin
-  gen_cc: generates C++ sources in addition to the ones from the plugin. 
+  gen_cc: generates C++ sources in addition to the ones from the plugin.
   gen_py: generates Python sources in addition to the ones from the plugin.
   outs: a list of labels of the expected outputs from the protocol compiler.
 """