This study presents the seasonal size distribution of particulate polycyclic aromatic hydrocarbons (PAHs), polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) and dioxin-like polychlorinated biphenyls (dl-PCBs) in the atmosphere. Particles were sampled from October 2009 to October 2010 on a seasonal basis using a cascade impactor collecting six size fractions at a rural and urban site in the Brno area, Czech Republic. Higher concentrations of PAHs, PCDD/Fs and dl-PCBs were observed in cold seasons at both sites, attributed to the seasonality of the gas-particle partitioning, the increase of emissions and the lower boundary mixing layer in winter. All of the compounds showed a strong accumulation in the fine fraction, with, on average, 71% of ΣPAHs, 73% of ΣPCDD/Fs and 60% of Σdl-PCBs associated with particles <0.95 μm. The human risk assessment via inhalation was addressed and followed the same pattern as for concentrations, with 41 and 7 times higher risk in winter compared to summer at the rural and urban sites, respectively. More than 70% of cancer risks of PAHs, PCDD/Fs and dl-PCBs was associated with particles <0.95 μm. Moreover, an overestimation of the cancer risk via inhalation of up to 50% occurred when the size distribution of related compounds was not considered.