The use of chemical flowsheeting software has become an integral part of the evaluation of the performance of fuel cell systems. There are, however, aspects that have to be kept in mind when comparing the results obtained in different system studies. If care is not taken, the obvious merit of one system over another could later be found to be induced by the software used for the study, more than by a superior systems layout. Some causes of these deviations are discussed based on a comparative system study, which was carried out using three different types of chemical simulation software. It is found that even though there appears to be no differences on an overall level, significant differences are found when examining at a more detailed level. The differences are found to be caused by differing thermodynamic data relating to the steam reforming section of the fuel cell system. Some of the deviations are also believed to be caused by convergence-related issues. (C) 2001 Elsevier Science B.V. All rights reserved.