diff --git a/Utilities/Doxygen/DoxygenConfig.cmake b/Utilities/Doxygen/DoxygenConfig.cmake
index b8f10746fe..945ec5bbf7 100644
--- a/Utilities/Doxygen/DoxygenConfig.cmake
+++ b/Utilities/Doxygen/DoxygenConfig.cmake
@@ -52,7 +52,9 @@ set(DOXYGEN_EXAMPLE_PATH "${DOXYGEN_TEST_DIRS}")
 set(DOXYGEN_EXAMPLE_PATTERNS "*.cxx")
 set(DOXYGEN_EXAMPLE_RECURSIVE "YES")
 set(DOXYGEN_IMAGE_PATH "${ITK_SOURCE_DIR}/Documentation/Art" "${ITK_BINARY_DIR}/Utilities/Doxygen/Modules")
-set(DOXYGEN_INPUT_FILTER "${ITK_DOXYGEN_INPUT_FILTER}")
+set(DOXYGEN_FILTER_PATTERNS
+    "*.h=${ITK_DOXYGEN_INPUT_FILTER}"
+    "*.cxx=${ITK_DOXYGEN_INPUT_FILTER}")
 set(DOXYGEN_FILTER_SOURCE_FILES "YES")
 set(DOXYGEN_SOURCE_BROWSER "YES")
 set(DOXYGEN_REFERENCED_BY_RELATION "YES")