A system and method for identifying leaks in a cathode sub-system of a fuel cell system. An air flow meter is provided up-stream of a compressor and monitors the air flowing into the compressor. When an air leakage diagnostic is commanded, a fuel cell stack by-pass valve and back-pressure valve are closed so that no air flows through or around the stack, and the recirculation valve is opened so that the air flows around the compressor. By knowing the leakage through the by-pass valve and the back-pressure valve, any flow above those values measured by the air flow meter gives an indication of air leakage out of the cathode sub-system components.