Protection of witnesses is a set economic, security, educational and psychological actions which the criminal justice system takes to improve participation of witnesses in judgment procedure. Such programs, a common process in the world countries and also international courts pertaining to organized crimes, terrorist crimes, crimes against humanity and war crimes, are performed in three major ways; protection-security, protective- psychological and programs to hide the identity of witnesses. On the other hand, today defensive rights of the accused is an integral part of a fair justice according to international, regional and internal laws and cannot be confined unless for a good reason; because this is a legacy the human society has achieved by hard endeavor and after centuries of judgment. At first sight, performing some of the programs like hiding the identity of witnesses and excessive protection of them is in sharp contrast with some rights of the accused like asking witnesses or the principle of equal opportunities. The issue can be minimized taking special actions and as a result, the principles of fair justice can somewhat be guaranteed.