diff --git a/CMakeLists.txt b/CMakeLists.txt
index dbfe93d57cf65..6ff156a60ed0e 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -350,30 +350,30 @@ endif()
 # Include directories
 #===============================================================================
 include_directories(BEFORE ${PROJECT_SOURCE_DIR})
-include_directories(${EIGEN3_INCLUDE_DIRS})
-include_directories(${FCL_INCLUDE_DIRS})
-include_directories(${ASSIMP_INCLUDE_DIRS})
-include_directories(${Boost_INCLUDE_DIRS})
-include_directories(${OPENGL_INCLUDE_DIR})
-include_directories(${GLUT_INCLUDE_DIR})
+include_directories(SYSTEM ${EIGEN3_INCLUDE_DIRS})
+include_directories(SYSTEM ${FCL_INCLUDE_DIRS})
+include_directories(SYSTEM ${ASSIMP_INCLUDE_DIRS})
+include_directories(SYSTEM ${Boost_INCLUDE_DIRS})
+include_directories(SYSTEM ${OPENGL_INCLUDE_DIR})
+include_directories(SYSTEM ${GLUT_INCLUDE_DIR})
 if(HAVE_BULLET_COLLISION)
-  include_directories(${BULLET_INCLUDE_DIRS})
+  include_directories(SYSTEM ${BULLET_INCLUDE_DIRS})
   add_definitions(${BULLET_CFLAGS})
 endif()
 
 if(NOT BUILD_CORE_ONLY)
-  include_directories(${FLANN_INCLUDE_DIRS})
-  include_directories(${urdfdom_INCLUDE_DIRS})
-  include_directories(${TINYXML_INCLUDE_DIRS})
-  include_directories(${TINYXML2_INCLUDE_DIRS})
+  include_directories(SYSTEM ${FLANN_INCLUDE_DIRS})
+  include_directories(SYSTEM ${urdfdom_INCLUDE_DIRS})
+  include_directories(SYSTEM ${TINYXML_INCLUDE_DIRS})
+  include_directories(SYSTEM ${TINYXML2_INCLUDE_DIRS})
   if(HAVE_NLOPT)
-    include_directories(${NLOPT_INCLUDE_DIRS})
+    include_directories(SYSTEM ${NLOPT_INCLUDE_DIRS})
   endif()
   if(HAVE_IPOPT)
-    include_directories(${IPOPT_INCLUDE_DIRS})
+    include_directories(SYSTEM ${IPOPT_INCLUDE_DIRS})
   endif()
   if(HAVE_SHARK)
-    include_directories(${SHARK_INCLUDE_DIRS})
+    include_directories(SYSTEM ${SHARK_INCLUDE_DIRS})
   endif()
 endif()