A wide range of infectious diseases may change their geographic range, seasonality and incidence due to climate change, but there is limited research exploring health vulnerabilities to climate change. In order to address this gap, pan-European vulnerability indices were developed for 2035 and 2055, based upon the definition vulnerability = impact/adaptive capacity. Future impacts were projected based upon changes in temperature and precipitation patterns, whilst adaptive capacity was developed from the results of a previous pan-European study. The results were plotted via ArcGISTM to EU regional (NUTS2) levels for 2035 and 2055 and ranked according to quintiles. The models demonstrate regional variations with respect to projected climate-related infectious disease challenges that they will face, and with respect to projected vulnerabilities after accounting for regional adaptive capacities. Regions with higher adaptive capacities, such as in Scandinavia and central Europe, will likely be better able to offset any climate change impacts and are thus generally less vulnerable than areas with lower adaptive capacities. The indices developed here provide public health planners with information to guide prioritisation of activities aimed at strengthening regional preparedness for the health impacts of climate change. There are, however, many limitations and uncertainties when modeling health vulnerabilities. To further advance the field, the importance of variables such as coping capacity and governance should be better accounted for, and there is the need to systematically collect and analyse the interlinkages between the numerous and ever-expanding environmental, socioeconomic, demographic and epidemiologic datasets so as to promote the public health capacity to detect, forecast, and prepare for the health threats due to climate change.