diff --git a/cmake/OpenCVPCHSupport.cmake b/cmake/OpenCVPCHSupport.cmake
index 7d7aacf00f..0084747817 100644
--- a/cmake/OpenCVPCHSupport.cmake
+++ b/cmake/OpenCVPCHSupport.cmake
@@ -69,6 +69,9 @@ MACRO(_PCH_GET_COMPILE_FLAGS _out_compile_flags)
     FOREACH(item ${DIRINC})
         if(item MATCHES "^${OpenCV_SOURCE_DIR}/modules/")
           LIST(APPEND ${_out_compile_flags} "${_PCH_include_prefix}\"${item}\"")
+        elseif(CMAKE_COMPILER_IS_GNUCXX AND NOT CMAKE_CXX_COMPILER_VERSION VERSION_LESS "6.0" AND
+               item MATCHES "/usr/include$")
+          # workaround for GCC 6.x bug
         else()
           LIST(APPEND ${_out_compile_flags} "${_PCH_isystem_prefix}\"${item}\"")
         endif()
@@ -78,6 +81,9 @@ MACRO(_PCH_GET_COMPILE_FLAGS _out_compile_flags)
     FOREACH(item ${DIRINC})
         if(item MATCHES "^${OpenCV_SOURCE_DIR}/modules/")
           LIST(APPEND ${_out_compile_flags} "${_PCH_include_prefix}\"${item}\"")
+        elseif(CMAKE_COMPILER_IS_GNUCXX AND NOT CMAKE_CXX_COMPILER_VERSION VERSION_LESS "6.0" AND
+               item MATCHES "/usr/include$")
+          # workaround for GCC 6.x bug
         else()
           LIST(APPEND ${_out_compile_flags} "${_PCH_isystem_prefix}\"${item}\"")
         endif()