diff --git a/CMakeLists.txt b/CMakeLists.txt
index b768d2a80ed..8ceea4e67a4 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -296,14 +296,14 @@ if(NOT PCL_SHARED_LIBS OR ((WIN32 AND NOT MINGW) AND NOT PCL_BUILD_WITH_FLANN_DY
   set(FLANN_USE_STATIC ON)
 endif()
 find_package(FLANN 1.7.0 REQUIRED)
-include_directories(${FLANN_INCLUDE_DIRS})
+include_directories(SYSTEM ${FLANN_INCLUDE_DIRS})
 
 # libusb-1.0
 option(WITH_LIBUSB "Build USB RGBD-Camera drivers" TRUE)
 if(WITH_LIBUSB)
   find_package(libusb-1.0)
   if(LIBUSB_1_FOUND)
-    include_directories("${LIBUSB_1_INCLUDE_DIR}")
+    include_directories(SYSTEM "${LIBUSB_1_INCLUDE_DIR}")
   endif()
 endif()
 
@@ -321,7 +321,7 @@ if(PKG_CONFIG_FOUND)
   pkg_check_modules(METSLIB metslib)
   if(METSLIB_FOUND)
     set(HAVE_METSLIB ON)
-    include_directories(${METSLIB_INCLUDE_DIRS})
+    include_directories(SYSTEM ${METSLIB_INCLUDE_DIRS})
   else()
     include_directories("${PCL_SOURCE_DIR}/recognition/include/pcl/recognition/3rdparty/")
   endif()
@@ -335,7 +335,7 @@ if(WITH_PNG)
   find_package(PNG)
   if(PNG_FOUND)
     set(HAVE_PNG ON)
-    include_directories("${PNG_INCLUDE_DIR}")
+    include_directories(SYSTEM "${PNG_INCLUDE_DIR}")
   endif()
 endif()
 
@@ -347,7 +347,7 @@ if(WITH_QHULL)
   endif()
   find_package(Qhull)
   if(QHULL_FOUND)
-    include_directories(${QHULL_INCLUDE_DIRS})
+    include_directories(SYSTEM ${QHULL_INCLUDE_DIRS})
   endif()
 endif()
 
diff --git a/apps/CMakeLists.txt b/apps/CMakeLists.txt
index aac0527dd43..f7a2a203669 100644
--- a/apps/CMakeLists.txt
+++ b/apps/CMakeLists.txt
@@ -188,7 +188,7 @@ endif() # VTK_FOUND
 # OpenGL and GLUT
 if(OPENGL_FOUND AND GLUT_FOUND)
   if(NOT WIN32)
-    include_directories("${OPENGL_INCLUDE_DIR}")
+    include_directories(SYSTEM "${OPENGL_INCLUDE_DIR}")
   endif()
   PCL_ADD_EXECUTABLE_OPT_BUNDLE(pcl_grabcut_2d "${SUBSYS_NAME}" src/grabcut_2d.cpp)
   target_link_libraries (pcl_grabcut_2d pcl_common pcl_io pcl_segmentation pcl_search GLUT::GLUT ${OPENGL_LIBRARIES})
diff --git a/doc/tutorials/content/sources/vfh_recognition/CMakeLists.txt b/doc/tutorials/content/sources/vfh_recognition/CMakeLists.txt
index cee6f69e499..fadb191d8e5 100644
--- a/doc/tutorials/content/sources/vfh_recognition/CMakeLists.txt
+++ b/doc/tutorials/content/sources/vfh_recognition/CMakeLists.txt
@@ -13,7 +13,7 @@ add_definitions(${PCL_DEFINITIONS})
 find_package(HDF5 REQUIRED)
 find_package(FLANN REQUIRED)
 
-include_directories(
+include_directories(SYSTEM
   ${FLANN_INCLUDE_DIRS}
   ${HDF5_INCLUDE_DIR}
 )
diff --git a/gpu/kinfu/CMakeLists.txt b/gpu/kinfu/CMakeLists.txt
index 245f0ed3fd9..ff2188c45bb 100644
--- a/gpu/kinfu/CMakeLists.txt
+++ b/gpu/kinfu/CMakeLists.txt
@@ -32,7 +32,8 @@ source_group("Source Files\\cuda" FILES ${cuda})
 source_group("Source Files" FILES ${srcs})
 
 set(LIB_NAME "pcl_${SUBSYS_NAME}")
-include_directories("${CMAKE_CURRENT_SOURCE_DIR}/include" "${CMAKE_CURRENT_SOURCE_DIR}/src" ${CUDA_INCLUDE_DIRS})
+include_directories("${CMAKE_CURRENT_SOURCE_DIR}/include" "${CMAKE_CURRENT_SOURCE_DIR}/src")
+include_directories(SYSTEM ${CUDA_INCLUDE_DIRS})
 
 if(UNIX OR APPLE)
   set(CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS}  "-Xcompiler;-fPIC;")
diff --git a/gpu/kinfu/tools/CMakeLists.txt b/gpu/kinfu/tools/CMakeLists.txt
index ce3f54e0404..c2b5c3ebe2d 100644
--- a/gpu/kinfu/tools/CMakeLists.txt
+++ b/gpu/kinfu/tools/CMakeLists.txt
@@ -14,7 +14,7 @@ else()
 endif()
 
 file(GLOB hdrs "*.h*")
-include_directories(${VTK_INCLUDE_DIRS} ${OPENNI_INCLUDE_DIRS})
+include_directories(SYSTEM ${VTK_INCLUDE_DIRS} ${OPENNI_INCLUDE_DIRS})
 
 ## KINECT FUSION
 set(the_target pcl_kinfu_app)
diff --git a/gpu/kinfu_large_scale/tools/CMakeLists.txt b/gpu/kinfu_large_scale/tools/CMakeLists.txt
index 14fc3117e82..9b15d9ac265 100644
--- a/gpu/kinfu_large_scale/tools/CMakeLists.txt
+++ b/gpu/kinfu_large_scale/tools/CMakeLists.txt
@@ -14,7 +14,7 @@ else()
 endif()
 
 file(GLOB hdrs "*.h*")
-include_directories(${VTK_INCLUDE_DIRS})
+include_directories(SYSTEM ${VTK_INCLUDE_DIRS})
 
 ## STANDALONE TEXTURE MAPPING
 set(the_target pcl_kinfu_largeScale_texture_output)
diff --git a/gpu/people/CMakeLists.txt b/gpu/people/CMakeLists.txt
index 174ef99a82c..7567338c539 100644
--- a/gpu/people/CMakeLists.txt
+++ b/gpu/people/CMakeLists.txt
@@ -48,11 +48,14 @@ source_group("Source files\\cuda" FILES ${srcs_cuda})
 source_group("Source files" FILES ${srcs})
 
 include_directories(
-  ${VTK_INCLUDE_DIRS}
   "${CMAKE_CURRENT_SOURCE_DIR}/include"
   "${CMAKE_CURRENT_SOURCE_DIR}/src"
   "${CMAKE_CURRENT_SOURCE_DIR}/src/cuda"
   "${CMAKE_CURRENT_SOURCE_DIR}/src/cuda/nvidia"
+)
+
+include_directories(SYSTEM
+  ${VTK_INCLUDE_DIRS}
   ${OpenCV_INCLUDE_DIRS}
   ${CUDA_INCLUDE_DIRS}
 )
diff --git a/gpu/people/tools/CMakeLists.txt b/gpu/people/tools/CMakeLists.txt
index 69c53814306..57f12101cf7 100644
--- a/gpu/people/tools/CMakeLists.txt
+++ b/gpu/people/tools/CMakeLists.txt
@@ -11,7 +11,7 @@ endif()
 
 set(the_target people_tracking)
 
-include_directories(${VTK_INCLUDE_DIRS})
+include_directories(SYSTEM ${VTK_INCLUDE_DIRS})
 
 #PCL_ADD_EXECUTABLE("${the_target}" "${SUBSYS_NAME}" people_tracking.cpp)
 #target_link_libraries("${the_target}" pcl_common pcl_filters pcl_kdtree pcl_segmentation pcl_kdtree pcl_gpu_people pcl_filters pcl_io pcl_visualization)
diff --git a/gpu/surface/CMakeLists.txt b/gpu/surface/CMakeLists.txt
index ac9dfd2adc7..fa5c68a4b76 100644
--- a/gpu/surface/CMakeLists.txt
+++ b/gpu/surface/CMakeLists.txt
@@ -26,7 +26,7 @@ source_group("Source Files\\cuda" FILES ${cuda})
 list(APPEND srcs ${utils} ${cuda})
 
 
-include_directories(${VTK_INCLUDE_DIRS})
+include_directories(SYSTEM ${VTK_INCLUDE_DIRS})
 
 set(LIB_NAME "pcl_${SUBSYS_NAME}")
 include_directories("${CMAKE_CURRENT_SOURCE_DIR}/include" "${CMAKE_CURRENT_SOURCE_DIR}/src" "${CMAKE_CURRENT_SOURCE_DIR}/src/cuda")
diff --git a/io/CMakeLists.txt b/io/CMakeLists.txt
index 6c030a4289b..3fb117a3783 100644
--- a/io/CMakeLists.txt
+++ b/io/CMakeLists.txt
@@ -249,7 +249,7 @@ endif()
 
 if(PCAP_FOUND)
   set(PCAP_DEFINES -DHAVE_PCAP)
-  include_directories(${PCAP_INCLUDE_DIRS})
+  include_directories(SYSTEM ${PCAP_INCLUDE_DIRS})
   add_definitions(${PCAP_DEFINES})
 endif()
 
diff --git a/simulation/tools/CMakeLists.txt b/simulation/tools/CMakeLists.txt
index 999aad730b8..08b16ddeef6 100644
--- a/simulation/tools/CMakeLists.txt
+++ b/simulation/tools/CMakeLists.txt
@@ -5,7 +5,7 @@ if(NOT (GLEW_FOUND AND GLUT_FOUND))
   return()
 endif()
 
-include_directories(${VTK_INCLUDE_DIRS})
+include_directories(SYSTEM ${VTK_INCLUDE_DIRS})
 
 PCL_ADD_EXECUTABLE(pcl_sim_viewer ${SUBSYS_NAME} sim_viewer.cpp)
 target_link_libraries (pcl_sim_viewer
diff --git a/test/io/CMakeLists.txt b/test/io/CMakeLists.txt
index 85f0e8d8922..1062f19f55e 100644
--- a/test/io/CMakeLists.txt
+++ b/test/io/CMakeLists.txt
@@ -35,7 +35,7 @@ PCL_ADD_TEST(io_ply_io test_ply_io
 
 # Uses VTK readers to verify
 if(VTK_FOUND AND NOT ANDROID)
-  include_directories(${VTK_INCLUDE_DIRS})
+  include_directories(SYSTEM ${VTK_INCLUDE_DIRS})
   PCL_ADD_TEST (io_ply_mesh_io test_ply_mesh_io
                 FILES test_ply_mesh_io.cpp
                 LINK_WITH pcl_gtest pcl_io
diff --git a/test/outofcore/CMakeLists.txt b/test/outofcore/CMakeLists.txt
index 6e7413d4c5e..4c0504d02cb 100644
--- a/test/outofcore/CMakeLists.txt
+++ b/test/outofcore/CMakeLists.txt
@@ -12,7 +12,7 @@ if(NOT build)
   return()
 endif()
 
-include_directories(${VTK_INCLUDE_DIRS})
+include_directories(SYSTEM ${VTK_INCLUDE_DIRS})
 PCL_ADD_TEST (outofcore_test test_outofcore
               FILES test_outofcore.cpp
               LINK_WITH pcl_gtest pcl_common pcl_io pcl_filters pcl_outofcore pcl_visualization)
diff --git a/test/people/CMakeLists.txt b/test/people/CMakeLists.txt
index 7d5a22eabbb..e9c4268700a 100644
--- a/test/people/CMakeLists.txt
+++ b/test/people/CMakeLists.txt
@@ -12,7 +12,7 @@ if(NOT build)
   return()
 endif()
 
-include_directories(${VTK_INCLUDE_DIRS})
+include_directories(SYSTEM ${VTK_INCLUDE_DIRS})
 PCL_ADD_TEST(a_people_detection_test test_people_detection
              FILES test_people_groundBasedPeopleDetectionApp.cpp
              LINK_WITH pcl_gtest pcl_common pcl_io pcl_kdtree pcl_search pcl_features pcl_sample_consensus pcl_filters pcl_io pcl_segmentation pcl_people
diff --git a/tools/CMakeLists.txt b/tools/CMakeLists.txt
index 02e573fa902..f82b57fd63b 100644
--- a/tools/CMakeLists.txt
+++ b/tools/CMakeLists.txt
@@ -270,7 +270,7 @@ target_link_libraries (pcl_transform_from_viewpoint pcl_common pcl_io pcl_regist
 
 find_package(tide QUIET)
 if(Tide_FOUND)
-  include_directories(${Tide_INCLUDE_DIRS})
+  include_directories(SYSTEM ${Tide_INCLUDE_DIRS})
   add_definitions(${Tide_DEFINITIONS})
   PCL_ADD_EXECUTABLE(pcl_video "${SUBSYS_NAME}" pcl_video.cpp)
   target_link_libraries(pcl_video pcl_common pcl_io pcl_visualization
diff --git a/visualization/CMakeLists.txt b/visualization/CMakeLists.txt
index 67c6ff6e10a..9d2df2158d8 100644
--- a/visualization/CMakeLists.txt
+++ b/visualization/CMakeLists.txt
@@ -23,7 +23,7 @@ endif()
 
 if(OPENGL_FOUND)
   if(OPENGL_INCLUDE_DIR)
-    include_directories("${OPENGL_INCLUDE_DIR}")
+    include_directories(SYSTEM "${OPENGL_INCLUDE_DIR}")
   endif()
   if(OPENGL_DEFINITIONS)
     add_definitions("${OPENGL_DEFINITIONS}")