diff --git a/scripts/cmake/CompilerSetup.cmake b/scripts/cmake/CompilerSetup.cmake
index 85032cdb3793d6af6ebd074c733138beb611b46e..22ba0e1afb9c6c19a1614f8697ba0bcf11949e95 100644
--- a/scripts/cmake/CompilerSetup.cmake
+++ b/scripts/cmake/CompilerSetup.cmake
@@ -4,9 +4,6 @@ INCLUDE(DisableCompilerFlag)
 SET_DEFAULT_BUILD_TYPE(Debug)
 INCLUDE(MSVCMultipleProcessCompile) # /MP switch (multi processor) for VS
 
-# Better Clang warning suppression, see http://www.openwalnut.org/issues/230
-SET( CMAKE_INCLUDE_SYSTEM_FLAG_CXX "-isystem" CACHE STRING "" FORCE )
-
 # Set compiler helper variables
 IF ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
     SET(COMPILER_IS_CLANG TRUE)
@@ -18,6 +15,11 @@ ELSEIF ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "MSVC")
     SET(COMPILER_IS_MSVC TRUE)
 ENDIF () # CMAKE_CXX_COMPILER_ID
 
+# Better Clang warning suppression, see http://www.openwalnut.org/issues/230
+IF(NOT COMPILER_IS_MSVC)
+	SET( CMAKE_INCLUDE_SYSTEM_FLAG_CXX "-isystem" CACHE STRING "" FORCE )
+ENDIF()
+
 # Set additional user-given compiler flags
 SET(CMAKE_CXX_FLAGS ${OGS_CXX_FLAGS})