The operating characteristic of a water-gas shift (WGS) reactor in a fuel cell system was investigated. Deactivation of the catalyst was identified in previous experiments during steady state and after startup/ shutdown, therefore reasons for the deactivation need to be investigated. Experiments on the system level revealed a correlation between deactivation and the fuel used. According to this correlation, a combination of a high amount of aromatic hydrocarbons in the fuel and a high boiling range had a more significant effect than a high amount of aromatics alone, followed by the single effect of a high boiling range. Furthermore, the presence of higher hydrocarbons from incomplete fuel conversion in the autothermal reformer (ATR) was associated with catalyst deactivation of the WGS reactor. To obtain a deeper understanding of the influence of higher hydrocarbons on catalyst activity, experiments were conducted with two commercial noble metal WGS catalysts using ideal and realistic reformate. Results under low-temperature-shift (LTS) conditions showed that both catalysts were only slightly influenced by the amount of higher hydrocarbons added in the steady state, as well as under shutdown conditions.