Abstract Background Public health is often affected by societal decisions that are not primarily about health. Climate change mitigation requires intensive actions to minimise greenhouse gas emissions in the future. Many of these actions take place in cities due to their traffic, buildings, and energy consumption. Active climate mitigation policies will also, aside of their long term global impacts, have short term local impacts, both positive and negative, on public health. Our main objective was to develop a generic open impact model to estimate health impacts of emissions due to heat and power consumption of buildings. In addition, the model should be usable for policy comparisons by non-health experts on city level with city-specific data, it should give guidance on the particular climate mitigation questions but at the same time increase understanding on the related health impacts and the model should follow the building stock in time, make comparisons between scenarios, propagate uncertainties, and scale to different levels of detail. We tested The functionalities of the model in two case cities, namely Kuopio and Basel. We estimated the health and climate impacts of two actual policies planned or implemented in the cities. The assessed policies were replacement of peat with wood chips in co-generation of district heat and power, and improved energy efficiency of buildings achieved by renovations. Results Health impacts were not large in the two cities, but also clear differences in implementation and predictability between the two tested policies were seen. Renovation policies can improve the energy efficiency of buildings and reduce greenhouse gas emissions significantly, but this requires systematic policy sustained for decades. In contrast, fuel changes in large district heating facilities may have rapid and large impacts on emissions. However, the life cycle impacts of different fuels is somewhat an open question. Conclusions In conclusion, we were able to develop a practical model for city-level assessments promoting evidence-based policy in general and health aspects in particular. Although all data and code is freely available, implementation of the current model version in a new city requires some modelling skills.