The experimental and theoretical studying of mechanical effects in running fuel cell is provided. It is shown that under optimized operating conditions it is possible to obtain the electrical performances of fuel cells at about 1 W cm−2. The further improvements can be achieved by means of mechanical effects. In particular, the influence of mechanical properties of seal joints and clamping bolt torques on the electrical performance is studied experimentally. It is demonstrated that rigid seal joints improve the electrical performance in comparison with the soft seal joints. Concerning the influence of the bolt torques, a certain optimal value is found for different types of MEA. The numerical modelling of mechanical stresses in running fuel cell is made. The developed model includes the main components of a real fuel cell (the membrane, the gas diffusion layers, the graphite plates, and the seal joints) and the clamping elements (the steel plates, the bolts, and the nuts). The operating conditions have been taken into account by imposing heat sources and humidity field. The results of modelling illustrate the main mechanical effects arising in the entire fuel cell. Copyright © 2009 John Wiley & Sons, Ltd.