diff --git a/Code/Mantid/Build/CMake/GNUSetup.cmake b/Code/Mantid/Build/CMake/GNUSetup.cmake
index fed25ef97dbce2e83176bdd49aa23b85277c2c56..df4711209a289fcf0aad3a0dd98c46b1c4b669b3 100644
--- a/Code/Mantid/Build/CMake/GNUSetup.cmake
+++ b/Code/Mantid/Build/CMake/GNUSetup.cmake
@@ -6,7 +6,7 @@
 # for that project.
 
 # Global warning flags.
-set( GNUFLAGS "-Wall -Wextra -Wconversion -Winit-self -Wmissing-prototypes -Wstrict-prototypes -Wshadow -Wpointer-arith -Wcast-qual -Wcast-align -fno-common" ) 
+set( GNUFLAGS "-Wall -Wextra -Wconversion -Winit-self -Wpointer-arith -Wcast-qual -Wcast-align -fno-common" ) 
 
 # Disable some warnings about deprecated headers and type conversions that
 # we can't do anything about