diff --git a/cmake/MacroRootDict.cmake b/cmake/MacroRootDict.cmake
index 385ee8a53..c66846a6c 100644
--- a/cmake/MacroRootDict.cmake
+++ b/cmake/MacroRootDict.cmake
@@ -45,6 +45,27 @@ ENDMACRO( PREPARE_ROOT_DICT_HEADERS )
 
 
 
+# Convert an absolute dictionary input header to the path used to include it.
+MACRO( ROOT_DICT_HEADER_INCLUDE_PATH _header _output )
+
+    SET( ${_output} "${_header}" )
+
+    IF( IS_ABSOLUTE "${_header}" )
+        FOREACH( _include_dir ${ROOT_DICT_INCLUDE_DIRS} )
+            IF( IS_ABSOLUTE "${_include_dir}" )
+                FILE( RELATIVE_PATH _relative_header "${_include_dir}" "${_header}" )
+                IF( NOT _relative_header MATCHES "^\\.\\." )
+                    SET( ${_output} "${_relative_header}" )
+                    BREAK()
+                ENDIF()
+            ENDIF()
+        ENDFOREACH()
+    ENDIF()
+
+ENDMACRO( ROOT_DICT_HEADER_INCLUDE_PATH )
+
+
+
 # ============================================================================
 # helper macro to generate Linkdef.h files for rootcint
 #
@@ -108,13 +129,22 @@ MACRO( GEN_ROOT_DICT_SOURCE _dict_src_filename )
         #SET( _dict_includes ${_dict_includes} -I${_inc} )
     ENDFOREACH()
 
+    # Use relative paths when invoking rootcint. Keep
+    # ROOT_DICT_INPUT_HEADERS unchanged below because CMake dependencies must
+    # refer to the original files.
+    SET( _dict_headers )
+    FOREACH( _header ${ROOT_DICT_INPUT_HEADERS} )
+        ROOT_DICT_HEADER_INCLUDE_PATH( "${_header}" _dict_header )
+        LIST( APPEND _dict_headers "${_dict_header}" )
+    ENDFOREACH()
+
     STRING( REPLACE "/" "_" _dict_src_filename_nosc ${_dict_src_filename} )
     SET( _dict_src_file ${ROOT_DICT_OUTPUT_DIR}/${_dict_src_filename_nosc} )
     STRING( REGEX REPLACE "^(.*)\\.(.*)$" "\\1.h" _dict_hdr_file "${_dict_src_file}" )
     ADD_CUSTOM_COMMAND(
         OUTPUT  ${_dict_src_file} ${_dict_hdr_file}
         COMMAND mkdir -p ${ROOT_DICT_OUTPUT_DIR}
-        COMMAND ${ROOT_rootcint_CMD} -f "${_dict_src_file}" -c ${ROOT_DICT_CINT_DEFINITIONS} ${_dict_includes} ${ROOT_DICT_INPUT_HEADERS}
+        COMMAND ${ROOT_rootcint_CMD} -f "${_dict_src_file}" -c ${ROOT_DICT_CINT_DEFINITIONS} ${_dict_includes} ${_dict_headers}
         WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
         DEPENDS ${ROOT_DICT_INPUT_HEADERS}
         COMMENT "generating: ${_dict_src_file} ${_dict_hdr_file}"
@@ -123,4 +153,3 @@ MACRO( GEN_ROOT_DICT_SOURCE _dict_src_filename )
 
 ENDMACRO()
 # ============================================================================
-
diff --git a/setup.sh b/setup.sh
index f4380f226..ced478483 100644
--- a/setup.sh
+++ b/setup.sh
@@ -13,5 +13,4 @@ for d in lib lib64; do
 done
 export PYTHONPATH=$LCIO/python:$PYTHONPATH
 alias pylcio='python $LCIO/python/pylcio.py'
-# Necessary for python bindings to work properly
-export CPATH=$LCIO:$LCIO/include:$CPATH
+export ROOT_INCLUDE_PATH="$LCIO/include${ROOT_INCLUDE_PATH:+:$ROOT_INCLUDE_PATH}"