There is an increasing attempt in the world to determine the exposures of children to environmental chemicals. To analyze the genotoxic effect of air pollution, micronucleus (MN) assay was carried out in buccal epithelial cells (BECs) of children living in an urban city of Turkey. Children from two schools at urban-traffic and suburban sites were investigated in summer and winter seasons for the determination of BEC-MN frequency (per mille) and frequency of BEC with MN (per mille). The same children were also recruited for lung function measurements within a MATRA project ("Together Towards Clean Air in Eskisehir and Iskenderun") Measured NO2 and SO2 concentrations did not exceed the European Union (EU) limit levels either in urban-traffic or suburban regions. Higher O3 concentrations were measured in the suburban site especially in the summer period. Particulate matter (PM2.5 and PM10) levels which did not differ statistically between two regions were above the EU limits in general. Although BEC-MN frequencies of children living in the suburban sites were higher in general, the difference between two regions was not significant either in the summer or winter periods. BEC-MN frequencies of the urban-traffic children were found to be significantly higher in summer period (mean ± SD, 2.68 ± 1.99) when compared to winter period (1.64 ± 1.59; p = 0.004). On the other hand, no seasonality was observed for the suburban children. Similar results have been obtained in the BEC frequency with MN in our study. In summer, BEC-MN frequencies were significantly increased with the decrease in pulmonary function levels based on forced expiratory flow between 25 and 75% of vital capacity (FEF25-75%) levels (p < 0.05). As a conclusion, children living in urban-traffic and suburban areas in the city of Eskişehir exhibited similar genotoxicity. Seasonal variation in genotoxicity may be interpreted as relatively high ozone levels and increasing time spent at outdoors in the summer.