diff --git a/configure b/configure
index a8e7bb77385..6cd5c2f3dbf 100755
--- a/configure
+++ b/configure
@@ -44,6 +44,13 @@ function bazel_clean_and_fetch() {
   bazel fetch "//tensorflow/... -//tensorflow/examples/android/..."
 }
 
+# Delete any leftover BUILD files from the Makefile build, which would interfere
+# with Bazel parsing.
+MAKEFILE_DOWNLOAD_DIR=tensorflow/contrib/makefile/downloads
+if [ -d "${MAKEFILE_DOWNLOAD_DIR}" ]; then
+  find ${MAKEFILE_DOWNLOAD_DIR} -type f -name '*BUILD' -delete
+fi
+
 ## Set up python-related environment settings
 while true; do
   fromuser=""
diff --git a/tensorflow/contrib/makefile/download_dependencies.sh b/tensorflow/contrib/makefile/download_dependencies.sh
index 7aebe18767b..58d1dc6f0af 100755
--- a/tensorflow/contrib/makefile/download_dependencies.sh
+++ b/tensorflow/contrib/makefile/download_dependencies.sh
@@ -44,6 +44,9 @@ download_and_extract() {
   echo "downloading ${url}" >&2
   mkdir -p "${dir}"
   curl -Ls "${url}" | tar -C "${dir}" --strip-components=1 -xz
+
+  # Delete any potential BUILD files, which would interfere with Bazel builds.
+  find "${dir}" -type f -name '*BUILD' -delete
 }
 
 download_and_extract "${EIGEN_URL}" "${DOWNLOADS_DIR}/eigen"