Recent studies have highlighted the presence of endotoxin in indoor air and its role in respiratory morbidities. Burning of household fuels including unprocessed wood and dried animal dung could be a major source of endotoxin in homes. We measured endotoxin levels in different size fractions of airborne particles (PM10, PM2.5, and PM1), and estimated the deposition of particle-bound endotoxin in the respiratory tract. The study was carried out in homes burning solid biomass fuel (n=35) and LPG (n=35). Sample filters were analyzed for endotoxin and organic carbon (OC) content. Household characteristics including temperature, relative humidity, and carbon dioxide levels were also recorded. Multivariate regression models were used to estimate the contributing factors for airborne endotoxin. Respiratory deposition doses were calculated using a computer-based model. We found a higher endotoxin concentration in PM2.5 fractions of the particle in both LPG (median: 110, interquartile range (IQR) 100-120 EU/m3) and biomass (median: 350, IQR: 315-430 EU/m3) burning homes. In the multivariate-adjusted model, burning of solid biomass fuel (β: 67; 95% CI: 10.5-124) emerged as the most significant predictor followed by OC (β: 4.7; 95% CI: 2.7-6.8), RH (β: 1.6; 95% CI: 0.76-2.4), and PM2.5 (β: 0.45; 95% CI: 0.11-0.78) for airborne endotoxin (P<0.05). We also observed an interaction between PM organic carbon content and household fuel in predicting the endotoxin levels. The model calculations showed that in biomass burning homes, total endotoxin deposition was higher among infants (59%) than in adult males (47%), of which at least 10% of inhaled endotoxin is deposited in the alveolar region of the lung. These results indicate that fine particles are significant contributors to the deposition of endotoxin in the alveolar region of the lung. Considering the paramount role of endotoxin exposure, and the source and timing of exposure on respiratory health, additional studies are warranted to guide evidence-based public health interventions.