diff --git a/cue.py b/cue.py
index a4ef650..1fc312e 100644
--- a/cue.py
+++ b/cue.py
@@ -737,6 +737,21 @@ CMPLR_CLASS = clang''')
 CC          = {0}{2}
 CCC         = {1}{2}'''.format(host_ccmplr_name, host_cppcmplr_name, host_cmplr_ver_suffix))
 
+        # Add additional flags to CONFIG_SITE
+        flags_text = ''
+        if 'USR_CPPFLAGS' in os.environ:
+            flags_text += '''
+USR_CPPFLAGS += {0}'''.format(os.environ['USR_CPPFLAGS'])
+        if 'USR_CFLAGS' in os.environ:
+            flags_text += '''
+USR_CFLAGS += {0}'''.format(os.environ['USR_CFLAGS'])
+        if 'USR_CXXFLAGS' in os.environ:
+            flags_text += '''
+USR_CXXFLAGS += {0}'''.format(os.environ['USR_CXXFLAGS'])
+        if flags_text:
+            with open(os.path.join(places['EPICS_BASE'], 'configure', 'CONFIG_SITE'), 'a') as f:
+                f.write(flags_text)
+
         fold_end('set.up.epics_build', 'Configuring EPICS build system')
 
     if not os.path.isdir(toolsdir):