diff --git a/infra/base-images/msan-builder/Dockerfile b/infra/base-images/msan-builder/Dockerfile
index bcbae7d49..54d4f212c 100644
--- a/infra/base-images/msan-builder/Dockerfile
+++ b/infra/base-images/msan-builder/Dockerfile
@@ -22,7 +22,7 @@ RUN apt-get update && apt-get install -y python dpkg-dev patchelf python-apt
 # Take all libraries from lib/msan
 RUN cp -R /usr/msan/lib/* /usr/lib/
 
-COPY compiler_wrapper.py msan_build.py wrapper_utils.py /usr/local/bin/
+COPY compiler_wrapper.py msan_build.py patch_build.py wrapper_utils.py /usr/local/bin/
 COPY packages /usr/local/bin/packages
 
 RUN mkdir /msan
diff --git a/infra/base-images/msan-builder/patch_build.py b/infra/base-images/msan-builder/patch_build.py
new file mode 100644
index 000000000..566015a75
--- /dev/null
+++ b/infra/base-images/msan-builder/patch_build.py
@@ -0,0 +1,134 @@
+#!/usr/bin/env python
+# Copyright 2017 Google Inc.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+################################################################################
+
+from __future__ import print_function
+import argparse
+import os
+import re
+import shutil
+import subprocess
+import sys
+
+INSTRUMENTED_LIBRARIES_DIRNAME = 'instrumented_libraries'
+MSAN_LIBS_PATH = '/msan'
+
+
+def IsElf(file_path):
+  """Whether if the file is an elf file."""
+  with open(file_path) as f:
+    return f.read(4) == '\x7fELF'
+
+
+def Ldd(binary_path):
+  """Run ldd on a file."""
+  try:
+    output = subprocess.check_output(['ldd', binary_path], stderr=subprocess.STDOUT)
+  except subprocess.CalledProcessError:
+    print('Failed to call ldd on', binary_path, file=sys.stderr)
+    return []
+
+  libs = []
+
+  OUTPUT_PATTERN = re.compile(r'\s*([^\s]+)\s*=>\s*([^\s]+)')
+  for line in output.splitlines():
+    match = OUTPUT_PATTERN.match(line)
+    if not match:
+      continue
+
+    libs.append((match.group(1), match.group(2)))
+
+  return libs
+
+
+def FindLib(path):
+  """Find instrumented version of lib."""
+  for lib_dir in os.listdir(MSAN_LIBS_PATH):
+    candidate_path = os.path.join(MSAN_LIBS_PATH, lib_dir, path[1:])
+    if os.path.exists(candidate_path):
+      return candidate_path
+
+  return None
+
+
+def PatchBinary(binary_path, instrumented_dir):
+  """Patch binary to link to instrumented libs."""
+  extra_rpaths = set()
+
+  for name, path in Ldd(binary_path):
+    if not os.path.isabs(path):
+      continue
+
+    instrumented_path = FindLib(path)
+    if not instrumented_path:
+      print('WARNING: Instrumented library not found for', path,
+            file=sys.stderr)
+      continue
+
+    target_path = os.path.join(instrumented_dir, path[1:])
+    if not os.path.exists(target_path):
+      print('Copying instrumented lib to', target_path)
+      target_dir = os.path.dirname(target_path)
+      if not os.path.exists(target_dir):
+        os.makedirs(target_dir)
+      shutil.copy2(instrumented_path, target_path)
+
+    extra_rpaths.add(
+        os.path.join('$ORIGIN', INSTRUMENTED_LIBRARIES_DIRNAME,
+                     os.path.dirname(path[1:])))
+
+  if not extra_rpaths:
+    return
+
+  existing_rpaths = subprocess.check_output(
+      ['patchelf', '--print-rpath', binary_path]).strip()
+  processed_rpaths = ':'.join(extra_rpaths)
+  if existing_rpaths:
+    processed_rpaths += ':' + existing_rpaths
+  print('Patching rpath for', binary_path, 'from', existing_rpaths, 'to',
+        processed_rpaths)
+
+  subprocess.check_call(
+      ['patchelf', '--force-rpath', '--set-rpath',
+       processed_rpaths, binary_path])
+
+
+def PatchBuild(output_directory):
+  """Patch build to use msan libs."""
+  instrumented_dir = os.path.join(output_directory,
+                                  INSTRUMENTED_LIBRARIES_DIRNAME)
+  os.mkdir(instrumented_dir)
+
+  for root_dir, _, filenames in os.walk(output_directory):
+    for filename in filenames:
+      file_path = os.path.join(root_dir, filename)
+      if not IsElf(file_path):
+        continue
+
+      PatchBinary(file_path, instrumented_dir)
+
+
+def main():
+  parser = argparse.ArgumentParser('patch_build.py', description='MSan build patcher.')
+  parser.add_argument('output_dir', help='Output directory.')
+
+  args = parser.parse_args()
+
+  PatchBuild(os.path.abspath(args.output_dir))
+
+
+if __name__ == '__main__':
+  main()