The overall water vapor balance and concentration distribution in the flow channels is a critical phenomenon affecting polymer electrolyte fuel cell (PEFC) performance. This paper presents, for the first time, results of a technique to measure in situ water vapor, nitrogen and oxygen distribution within the gas channels of an operating PEFC. The use of a gas chromatograph (GC) to measure high levels of water saturation directly, without dehumidification of the flow stream, is a unique aspect of this work. Following careful calibration and instrumentation, a gas chromatograph (GC) was interfaced directly to the fuel cell at various locations along the serpentine anode and cathode flow paths of a specially designed fuel cell. The 50cm² active area fuel cell also permits simultaneous current distribution measurements via the segmented collector plate approach. The on-line GC method allows discrete measurements of the water vapor content up to a fully saturated condition about every 2 minutes. Water vapor and other species distribution data are shown for several inlet relative humidities on the anode and cathode for different cell voltages. For the thin electrolyte membranes used (51μm), there is little functional dependence of the anode gas channel water distribution on current output. For thin membranes, this indicates that there is little gradient in the water activity between anode and cathode, indicating diffusion can offset electro-osmotic drag under these circumstances (i<0.5A/cm²). This technique can be used for detailed studies on water distribution and transport in the PEFC.