We present an overview of the program on the evaluation methodology for proliferation resistance and physical protection (PR&PP) of advanced nuclear energy systems (NESs) sponsored by the Generation IV International Forum (GIF). For a proposed NES design, the methodology defines a set of challenges, analyzes system response to these challenges, and assesses outcomes. The challenges to the NES are the threats posed by potential actors (proliferant States or sub-national adversaries). The characteristics of Generation IV systems, both technical and institutional, are used to evaluate the response of the system and to determine its resistance against proliferation threats and robustness against sabotage and terrorism threats. The outcomes of the system response are expressed in terms of a set of measures, which are the high-level PR&PP characteristics of the NES. The methodology is organized to allow evaluations to be performed at the earliest stages of system design and to become more detailed and more representative as the design progresses. It can thus be used to enable a program in safeguards by design or to enhance the conceptual design process of an NES with regard to intrinsic features for PR&PP.