To meet the power density, reliability and cost requirements that will enable a widespread use of fuel cells, many research activities focus on an understanding of the thermodynamics as well as the fluid mechanical and electrochemical processes within a fuel cell. To date, a wide range of experimental diagnostics is imperative not only to help a fundamental understanding of fuel cell dynamics but also to provide benchmark-quality data for modeling research. This paper reviews various tools for diagnosing polymer electrolyte membrane (PEM) fuel cells and stacks, and attempts to incorporate the most recent technical advances in PEM fuel cell diagnosis. In Part I of the review we covered electrochemical techniques. In Part II, we review various physical/chemical methods and outline the principle, experimental implementation and data processing of each technique. Capabilities and weaknesses of these techniques are also discussed. (c) 2008 International Association for Hydrogen Energy. Published by Elsevier Ltd. All rights reserved.