Aeroallergen pollen can influence human health, through the response of the immune system, degrading the quality of life. The most common allergic reaction is the hay fever, a highly prevalent and chronic disease, which can affect up to 50% of the population in some cases, especially in the developing countries. Only a moderate number of estimates of the pollen health effects have been made worldwide while in Greece the relevant studies are scarce to non-existing. In Greece one of the most significant taxa are Quercus, but estimations of its pollen concentrations as well its consequent health effects have never been realized before. In this study the potential health effects from Quercus pollen in the greater area of Thessaloniki are estimated. The estimation is implemented with a custom modeling system, comprising the meteorological model WRF, the Natural Emissions Model (NEMO) for the calculation of the Quercus pollen emissions and the chemistry-transport model CAMx for the advection and the deposition of the pollen particles. The period of 2016 with the highest potential is selected, based on the available measurements for the area of interest. The modeling system is evaluated with meteorological and biological measurements, indicating a satisfactory performance on the surface Quercus pollen concentrations. The modeling system is finally utilized for the estimation of exposure levels in the greater area of Thessaloniki.