Investigation of microbial communities in the indoor environment is critically important as majority of human life is spent indoors. Airborne microbial flora and their pyrogenic substances can impact human health. They have so far been insufficiently characterized. Here, we quantify bioaerosol concentration and diversity in both indoor and outdoor air of rural households in South India and statistically determine the significant predictor variables influencing them. The median concentration of bacterial and fungal aerosols in indoor air (n = 36 households) was 1031 colony forming units (CFU) m−3 and 580 CFU m−3, respectively, and in outdoor air was 742 CFU m−3 and 680 CFU m−3, respectively. Bacterial species were comprised of the four major phyla Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes, and fungal species of Ascomycota, Basidiomycota, and Zygomycota, in both indoor and outdoor air. Multivariable linear regression revealed that outdoor bacterial concentration, the number of house inhabitants, indoor temperature, age of the homes and use of biomass (cow dung or firewood) as cooking fuel were significant predictor variables influencing concentrations of bacteria in the indoor air. The significant predictor variables influencing indoor endotoxin concentrations were indoor bacterial concentration, indoor meteorology (temperature and relative humidity), and use of biomass as cooking fuel. Outdoor fungal concentration was the significant predictor variable influencing fungal concentration in indoor air. Endotoxin concentrations in indoor air ranged from 1.23 to 20.7 EU m−3. Quantitative microbial risk assessment (QMRA) model revealed a probability of infection of resident women from B. anthracis to be 0.0009 to 0.010. © 2020 Elsevier Ltd