Atmospheric aerosol samples were studied during wintry conditions at three Hungarian locations (rural background, urban background, traffic site). Ratio of biomass burning and fossil fuel related aerosol were highly different at the sampling points. Cyto- and genotoxicity of the samples were measured by using Pseudomonas putida growth inhibition test and Ames test, respectively. Dominant particle emission sources were apportioned through tracer heavy metal content measurement, optically and thermo-optically methods. According to the results, both ecotoxicity parameters are strongly emission source dependent; the higher the ratio of the biomass burning related carbonaceous aerosol the higher the cytotoxicity and the higher the ratio of the fossil fuel related carbonaceous aerosol the higher the genotoxicity. Cytotoxicity showed positive correlation with carbonaceous aerosol related to biomass burning (R2 = 0.74) and negative with lead content of the samples (R2 = –0.56). Genotoxicity showed positive correlation with carbonaceous aerosol related to traffic (R2 = 0.42) and cadmium content of the samples (R2 = 0.74). At the same time, it showed negative correlation with organic/elemental carbon ratio of the samples (R2 = –0.43).