The wide use of subway system by citizens underlines the importance of hygienic issues including indoor air pollution in these public places especially in metro stations. The aim of this study was to investigate the bacterial contamination in indoor and outdoor air of two metro stations (Imam Khomeini and Sadeghiyeh stations) in Tehran subway system. In this cross sectional study, three sampling locations were selected in each station. Also, sampling was conducted in indoor air of two types (old and new) of trains. The range of bacterial colony count was 35-1501 CFU/m³. Maximum and minimum bacterial contamination levels in Imam Khomeini and Sadeghiyeh platform stations were averagely 1073 CFU/m³ and 242 CFU/m³, respectively.14 bacterial species and genera were isolated, among them the dominant species were Staphylococcus epidermidis, Micrococcus luteus and Bacillus spp. Results showed that bacterial concentrations in indoor air were higher than the outdoor air, also the bacterial counts correlated significantly with number of the passengers (p<0.001) and air temperature (p<0.001).