Genotoxicity of indoor air pollution from biomass fuel use has been examined in 132 biomass users (median age 34 years) and 85 age-matched control women from eastern India who used the cleaner fuel liquefied petroleum gas (LPG) to cook. Micronucleus (MN) frequency was evaluated in buccal (BEC) and airway epithelial cells (AEC); DNA damage was examined by comet assay in peripheral blood lymphocytes (PBL); and expressions of γ-H2AX, Mre11 and Ku70 proteins were localized in AEC and PBL by immunocytochemistry. Reactive oxygen species (ROS) generation in leukocytes was measured by flow cytometry, and the levels of superoxide dismutase (SOD) and total antioxidant status (TAS) in blood were measured by spectrophotometry. Real-time aerosol monitor was used to measure particulate pollutants in indoor air. Compared with controls, biomass users had increased frequencies of micronucleated cells in BEC (3.5 vs. 1.7, p <0.001) and AEC (4.54 vs. 1.86, p <0.001), and greater comet tail % DNA (18.6 vs. 11.7%, p <0.01), tail length (45.5 vs. 31.4μm, p <0.01) and olive tail moment (4.0 vs. 1.4, p <0.01) in PBL. Moreover, biomass users had more γ-H2AX-positive nuclei in PBL (49.5 vs. 8.5%, p <0.01) and AEC (11.3 vs. 2.9%, p <0.01) along with higher expression of DNA repair proteins Mre11 and Ku70 in these cells, suggesting stimulation of DNA repair mechanism. Biomass users showed rise in ROS generation and depletion of SOD and TAS. Biomass-using households had 2–4 times more particulate matter with diameter less than 10 and 2.5μm in indoor air, and MN frequency and comet tail % DNA were positively associated with these pollutants after controlling potential confounders. Thus, chronic exposure to biomass smoke causes chromosomal and DNA damage and upregulation of DNA repair mechanism.