Use -isystem instead of -I with CMake

Yes you force a path to be a system include by using the optional SYSTEM flag

include_directories(SYSTEM path)

http://www.cmake.org/cmake/help/cmake-2-8-docs.html#command:include_directories

Starting with CMake 2.8.12 you can use the new target_include_directories to include system directory includes at the target level, while leveraging the new usage requirement features of cmake:

target_include_directories(foo SYSTEM PUBLIC path)

Now target foo will use path as a system include, and anything that links to foo will also use path as automatically as a system include. You can control the propagation of these usage requirements by changing the PUBLIC keyword to PRIVATE or INTERFACE.

http://cmake.org/cmake/help/v2.8.12/cmake.html#command:target_include_directories

As stated already, the correct way to include system paths is:

include_directories(SYSTEM path1 path2)

However as of CMake 2.8.4 and Makefiles, This is only used for C++ and not C, I looked into it and GNU.cmake does not initialize: CMAKE_INCLUDE_SYSTEM_FLAG_C

So you can set this yourself right after calling project().

if(CMAKE_COMPILER_IS_GNUCC)
  set(CMAKE_INCLUDE_SYSTEM_FLAG_C "-isystem ")
endif()

Update:

The CMake developers have fixed this in 2.8.5