In this paper, we experimentally investigated two high temperature polymer electrolyte membrane fuel cell (HT-PEMFC) stacks for their response to the presence of reformate impurities in an anode gas stream. The investigation was aimed at characterizing the effects of reformate impurities at the stack level, including in humidified conditions and identifying fault features for diagnosis purposes. Two HT-PEMFC stacks of 37 cells each with active areas of 165 cm2 were used with one stack containing a pre-doped membrane with a woven gas diffusion layer (GDL) and the other containing a post-doped membrane with non-woven GDL. Polarization curves and galvanostatic electrochemical impedance spectroscopy (EIS) were used for characterization. We found that both N2 dilution and impurities in the anode feed affected mainly the charge transfer losses, especially on the anode side. We also found that humidification alleviated the poisoning effects of the impurities in the stack with pre-doped membrane electrode assemblies (MEA) and woven GDL but had detrimental effects on the stack with post-doped MEAs and non-woven GDL. We demonstrated that pure and dry hydrogen operation at the end of the tests resulted in significant recovery of the performance losses due to impurities for both stacks even after the humidified reformate operation. This implies that there was only limited acid loss during the test period of around 150 h for each stack.