Objectives Indoor air pollutants from biomass combustion pose a risk for respiratory diseases in children. It is plausible that distinct differences in the indoor air quality (IAQ) exist between urban and rural areas in developing countries since the living environment between these two areas are quite different. We have investigated possible differences in IAQ in urban and rural Dhaka, Bangladesh and the association of such differences with the incidence of respiratory and some non-respiratory symptoms in children of families using biomass fuel. Methods Indoor air concentrations of carbon monoxide (CO), carbon dioxide (CO 2 ), dust particles, volatile organic compounds (VOCs), and nitrogen dioxide were measured once in the winter and once in the summer of 2008. Health data on 51 urban and 51 rural children under 5 years of age from 51 families in each area were collected once a week starting in the winter and continuing to the summer of 2008.Results Mean concentrations of CO, CO 2, , dust particles, and major VOCs were significantly higher in urban kitchens than in rural ones (p \ 0.05). The incidence rate ratio (IRR) suggests that compared to the urban children, the children in the rural area suffered significantly more from respiratory symptoms [IRR 1.63, 95% confidence interval (CI) 1.62-1.64], skin itchiness (IRR 3.3, 95% CI 1.9-5.7), and diarrhea (IRR 1.8, 95% CI 1.4-2.4), while fewer experienced fever (IRR 0.5, 95% CI 0.4-0.6). No difference was observed for other symptoms. Conclusions We found lower IAQ in the homes of urban biomass fuel-users compared to rural ones in Bangladesh but could not attribute the occurrence of respiratory symptoms among children to the measured IAQ. Other factors may be involved.