diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 96c89fef..0e37e487 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -229,18 +229,10 @@ list(APPEND CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/external)
 #2. if ONNX_CUSTOM_PROTOC_EXECUTABLE is not set, Compile everything(including protoc) from source code.
 
 
-# use protobuf as a submodule
-add_subdirectory(${PROJECT_SOURCE_DIR}/external/protobuf/cmake EXCLUDE_FROM_ALL)
-set_target_properties(libprotobuf PROPERTIES FOLDER "External/Protobuf")
-set_target_properties(libprotobuf-lite PROPERTIES FOLDER "External/Protobuf")
-set_target_properties(libprotoc PROPERTIES FOLDER "External/Protobuf")
-set_target_properties(protoc PROPERTIES FOLDER "External/Protobuf")
-if (onnxruntime_USE_FULL_PROTOBUF)
-  add_library(protobuf::libprotobuf ALIAS libprotobuf)
-else()
-  add_library(protobuf::libprotobuf ALIAS libprotobuf-lite)
-endif()
-add_executable(protobuf::protoc ALIAS protoc)
+find_package(PkgConfig)
+pkg_check_modules(PROTOBUF REQUIRED IMPORTED_TARGET GLOBAL protobuf)
+add_library(libprotobuf ALIAS PkgConfig::PROTOBUF)
+add_library(protobuf::libprotobuf ALIAS PkgConfig::PROTOBUF)
 include(protobuf_function.cmake)
 
 
@@ -282,8 +274,6 @@ set(ONNXRUNTIME_INCLUDE_DIR ${REPO_ROOT}/include/onnxruntime)
 
 add_subdirectory(external/date EXCLUDE_FROM_ALL)
 add_subdirectory(external/gsl EXCLUDE_FROM_ALL)
-add_subdirectory(external/re2 EXCLUDE_FROM_ALL)
-set_target_properties(re2 PROPERTIES FOLDER "External/re2")
 add_library(gsl ALIAS GSL)
 
 # bounds checking behavior.
@@ -306,7 +296,7 @@ function(onnxruntime_add_include_to_target dst_target)
     endforeach()
 endfunction()
 
-set(onnxruntime_EXTERNAL_DEPENDENCIES gsl onnx_proto re2)
+set(onnxruntime_EXTERNAL_DEPENDENCIES gsl onnx_proto)
 
 # TVM
 if (onnxruntime_USE_TVM)
@@ -620,15 +605,10 @@ if (onnxruntime_BUILD_UNIT_TESTS)
   # turned ON by the previous step when building a shared lib
   set(CMAKE_SKIP_BUILD_RPATH OFF)
   # gtest and gmock
-  add_subdirectory(${PROJECT_SOURCE_DIR}/external/googletest EXCLUDE_FROM_ALL)
-  set_target_properties(gmock PROPERTIES FOLDER "External/GTest")
-  set_target_properties(gmock_main PROPERTIES FOLDER "External/GTest")
-  set_target_properties(gtest PROPERTIES FOLDER "External/GTest")
-  set_target_properties(gtest_main PROPERTIES FOLDER "External/GTest")
-  if(UNIX)
-    target_compile_options(gmock PRIVATE "-w")
-    target_compile_options(gtest PRIVATE "-w")
-  endif()
+  pkg_check_modules(GTEST REQUIRED IMPORTED_TARGET GLOBAL gtest)
+  pkg_check_modules(GMOCK REQUIRED IMPORTED_TARGET GLOBAL gmock)
+  add_library(gtest ALIAS PkgConfig::GTEST)
+  add_library(gmock ALIAS PkgConfig::GMOCK)
   include(onnxruntime_unittests.cmake)
 endif()
 
diff --git a/cmake/onnxruntime_python.cmake b/cmake/onnxruntime_python.cmake
index ace16b1b..c76ebde4 100644
--- a/cmake/onnxruntime_python.cmake
+++ b/cmake/onnxruntime_python.cmake
@@ -1,7 +1,6 @@
 # Copyright (c) Microsoft Corporation. All rights reserved.
 # Licensed under the MIT License.
 
-include(pybind11)
 FIND_PACKAGE(NumPy)
 
 if(NOT PYTHON_INCLUDE_DIR)
@@ -83,7 +82,6 @@ set(onnxruntime_pybind11_state_libs
 
 set(onnxruntime_pybind11_state_dependencies
     ${onnxruntime_EXTERNAL_DEPENDENCIES}
-    pybind11
 )
 
 add_dependencies(onnxruntime_pybind11_state ${onnxruntime_pybind11_state_dependencies})
diff --git a/onnxruntime/core/util/protobuf_parsing_utils.cc b/onnxruntime/core/util/protobuf_parsing_utils.cc
index 4e46d0ef..8638f353 100644
--- a/onnxruntime/core/util/protobuf_parsing_utils.cc
+++ b/onnxruntime/core/util/protobuf_parsing_utils.cc
@@ -49,7 +49,6 @@
 #include <google/protobuf/stubs/common.h>
 #include <google/protobuf/stubs/logging.h>
 #include <google/protobuf/stubs/stl_util.h>
-#include <google/protobuf/stubs/io_win32.h>
 #include "protobuf_parsing_utils.h"
 #include <string.h>