This experimental paper presents a study of gas-liquid two phase flow in rectangular channels of 500μm × 45μm and 23.7mm long with different wall conditions of hydrophilic and hydrophobic surface, in order to investigate the flow structures and the corresponding friction factors of simulated microchannels of PEMFC. The main flow in the channel is air and liquid water is injected at a single or several discrete locations in one side wall of the channel. The flow structure of liquid water in hydrophilic wall conditioned channel starts from wavy flow, develops to stable stratified film flow, and then transits to unstable fluctuating film flow, as the pressure drop and the flow velocity of air increase from around 10 kPa to over 100 kPa. The flow structure in hydrophobic channel develops from the slug flow to slug-and-film flow with increasing pressure drop and flow velocity. The pressure drop for single phase flow is measured for a base line study, and the fRe product is in close agreement with the theoretical value (/Ke=85) of the conventional laminar flow of aspect ratio 1:11. At the low range of water injection rate, the gas phase fRe product of the two phase flow based on the whole channel area was not substantially affected by the water introduction. However, as the water injection rate increases up to 100 μL/min, the gas phase fRe product based on the whole channel area deviates highly from the single phase theoretical value. The gas phase fRe product with the actual gas phase area corrected by the liquid phase film thickness agrees with the single phase theoretical value.