diff --git a/CMakeLists.txt b/CMakeLists.txt
index dc4ab1504399a61fb25b1743789ed5c065a5bd7b..42576d9e7cf5f4591427fe653d7ff452546e4011 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -50,9 +50,9 @@ OPTION (BUILD_UNIT_TESTS "Build the unitary tests" ON)
 
 FINDPYTHON()
 
-INCLUDE_DIRECTORIES(SYSTEM ${PYTHON_INCLUDE_DIRS})
+INCLUDE_DIRECTORIES(${PYTHON_INCLUDE_DIRS})
 FIND_NUMPY()
-INCLUDE_DIRECTORIES(SYSTEM ${NUMPY_INCLUDE_DIRS})
+INCLUDE_DIRECTORIES(${NUMPY_INCLUDE_DIRS})
 
 # ----------------------------------------------------
 # --- DEPENDANCIES -----------------------------------
@@ -137,8 +137,8 @@ ADD_SUBDIRECTORY(python)
 ADD_SUBDIRECTORY(unittest)
 
 PKG_CONFIG_APPEND_LIBS(${PROJECT_NAME})
-PKG_CONFIG_APPEND_CFLAGS("-isystem${PYTHON_INCLUDE_DIRS}")
-PKG_CONFIG_APPEND_CFLAGS("-isystem${NUMPY_INCLUDE_DIRS}")
+PKG_CONFIG_APPEND_CFLAGS("-I${PYTHON_INCLUDE_DIRS}")
+PKG_CONFIG_APPEND_CFLAGS("-I${NUMPY_INCLUDE_DIRS}")
 PKG_CONFIG_APPEND_BOOST_LIBS(${BOOST_COMPONENTS})
 
 SETUP_PROJECT_FINALIZE()