Heat stress is a current public health concern during the warm months in many urban areas. Climate change and increasing urbanization are expected to worsen this concern, with some locations being more vulnerable than others. The aim of this study was to determine the short-term effect of heat on mortality in the two most populated cities in Portugal: Lisbon and Oporto. Each city was assessed for specific heat stress threshold above which heat-related mortality becomes significant. A Poisson generalized estimating equations (GEE) model was used to estimate the impact of maximum apparent temperature (ATmax) and maximum temperature (Tmax) on daily mortality, in the summer season. Data show ATmax thresholds of 30.4 degrees C for Lisbon and 26.3 degrees C for Oporto, and Tmax thresholds of 29.3 degrees C and 25.0 degrees C, respectively. For every 1 degrees C elevation in ATmax above the city-specific threshold, all-cause mortality rate rose by 7.13% (95% CI: 5.9; 8.4) in Lisbon and 4.31% (95% CI: 3.2; 5.4) in Oporto. The Tmax threshold increases were 5.6% (95% CI: 4.6; 6.6) in Lisbon and 3% (95% CI: 2.0, 3.9) in Oporto. In both cities, stronger associations were found for respiratory diseases and the elderly group was the most vulnerable. This study confirmed that elevated temperatures have a considerable impact on daily mortality frequency in the two most urbanized areas in Portugal. Our results also provide useful data for policymakers to better prepare local actions to mitigate and reduce the health risks associated with high temperatures.