İn this study, micro-cogeneration application is used to increase the efficiency of Proton Exchange Membrane Fuel Cell PEMFC systems and effect of different operation temperatures on system performance is observed. For this reason, two different PEMFC systems were comparatively studied operating at 70o C and 160o C, respectively. Micro-cogeneration system design has done considering experimentally determined current density, power and temperature values. Since the amount of heat extracted from each PEMFC system is different related to the operating temperatures, different heat transfer fluids have been used for the cooling systems. These systems are designed for utilization of electricity and hot water for Atılım University Hydrogen Energy Laboratory. Heat loss calculation is made for the laboratory and thermal energy needed for heating the laboratory is calculated. Parallel to the design calculations, simple payback times for PEMFCs with micro-cogeneration applications were determined. LT-PEMFC and HT-PEMFC systems have 402 W and 456 W thermal powers respectively and 87.4 % and 92.8 % total cogeneration efficiencies were calculated for each system respectively. For each system maximum water temperatures and flow rates are calculated as a result of micro-cogeneration application. HT-PEMFC system has found to be capable of higher amount of heating. Even LT-PEMFC system has a lower thermal power and efficiency; it is determined to be more economical and has a lower pay pack time then HT-PEMFC system. For both systems, necessary number of stacks to be used for laboratory heating is calculated as four.