Low temperature hydrogen fuel cells are electrochemical devices which offer a promising alternative to traditional power sources. Fuel cells produce electricity with a reaction of the fuel (hydrogen) and air. Fuel cells have the advantage of being clean; only producing water and heat as by products. The efficiency of a fuel cell varies depending on the type; SOFC with CHP for example, can have a system efficiency of up to 65%. What the Authors present here is a comparison between three different configurations of flow plates of a proton exchange membrane fuel cell, the manufacturer’s serpentine flow plate and two new configurations; the maze flow plate and the parallel flow plate. A study of the input parameters affecting output responses of voltage, current, power and efficiency of a fuel cell is performed through experimentation. The results were taken from direct readings of the fuel cell and from polarisation curves produced. This information was then analysed through a design of experiment to investigate the effects of the changing parameters on different configurations of the fuel cell’s flow plates. The results indicate that, in relation to current and voltage response of the polarisation curve and the corresponding graphs produced from the DOE, the serpentine flow plate design is a much more effective design than the maze or parallel flow plate design. It was noted that the parallel flow plate performed reasonably well at higher pressures but over all statically the serpentine flow plate performed better.