Calorimeters can be miniaturized to the point where they can be integrated into platforms such as micrototal analysis systems (TAS) or lab-on-chip. Models of microscale calorimeters currently fail to account for variations of material properties known to be present in thin films. This study attempts to address this deficiency. Resistivity and absolute Seebeck coefficient of gold and nickel thin films were found to vary linearly with the inverse of film thickness in the submicron range. Thin-film thermopiles composed of gold and nickel were fabricated and their resistance and sensitivity were measured. Our results show that thinfilm effects can introduce a 15% decrease in sensitivity (temperature-to-voltage conversion ratio) and a 30% decrease in resolution (smallest resolvable temperature difference). Introducing material properties variation with film thickness into models of thermopile performance resulted in improved estimates. Modelling results suggest that grain boundary scattering is a strong contributor to the observed filmthickness-related change of resistivity and Seebeck coefficient. These observations have implications for improving the design and fabrication of thermopile-based, and other microfabricated, microscale calorimeters.