Poor indoor air quality can be particularly harmful to children and interfere with the growth of their lung function as they spend much of their time indoors. In order to understand the mechanism of exposure in the airways, biomarkers were used as a surrogate for biological responses towards indoor air pollutants. This study aims to investigate the association between indoor air pollutants (PM 2.5 , PM 10 and NO 2 ) among school children in different area of urban and rural site in Klang Valley. A cross sectional comparative study was conducted among 430 healthy schoolchildren from a national primary school. Methods involved questionnaires based on American Thoracic Society and sputum samples for biomarkers assay. Indoor exposure to PM 2.5 and PM 10 (Dust Trak Aerosol Monitor) and NO 2 (LaMotte Air Sampler) were measured in the classroom. Mean concentration of PM 2.5 (50.72 µg/m 3 ) in urban schools were significantly higher compared to rural (28.36 µg/m 3 ) school. Similar trend found in indoor level of PM 10 in urban and rural schools with 87.04 µg/m 3 and 56.76 µg/m 3 respectively. The mean exposure level of NO 2 of urban schools (0.12 ppm) is nearly 4 times higher than the level in rural areas (0.032 ppm). A significant association was found between indoor air concentrations (PM 2.5 and PM 10 ) with TNF-alpha level. Children from rural areas are exposed to less air pollutants compared to those from urban area and this study also suggests that higher exposure to PM 2.5 , PM 10 and NO 2 are associated with increasing of TNF-alpha level.