A method and system for detecting imperfections in a membrane electrode assembly of an electrochemical fuel cell, and more particularly for detecting defects within a proton exchange membrane in a membrane electrode assembly which is optionally sandwiched between conductive diffusion media layers or between conductive diffusion layers with at least one rigid solid that is transparent to infrared radiation. A potential voltage is applied across the membrane and the presence of a defect and preferably the location of a defect is determined by monitoring variations in intensity level of infrared radiation emitted from a surface of the membrane electrode assembly.