Background: About half of the world's population is exposed to smoke from burning biomass fuels at home. The high airborne particulate levels in these homes and the health burden of exposure to this smoke is well described. Burning unprocessed biological material such as wood and dried animal dung may also produce high indoor endotoxin concentrations. This study measured airborne endotoxin levels in homes burning different biomass fuels. Methods: Air sampling was carried out in homes burning wood or dried animal dung in Nepal (n=31) and wood, charcoal or crop residues in Malawi (n=38). Filters were analysed for endotoxin content expressed as airborne endotoxin concentration and endotoxin per mass of airborne particulate. Results: Airborne endotoxin concentrations were high. Averaged over 24h in Malawian homes, median concentrations of total inhalable endotoxin were 24 EU/m3 in charcoal-burning homes and 40 EU/m3 in wood-burning homes. Short cooking-time samples collected in Nepal produced median values of 43 EU/m3 in wood-burning homes and 365 EU/m3 in dung-burning homes suggesting increasing levels with movement down the energy ladder of unprocessed solid fuels. Conclusions: Airborne endotoxin concentrations in homes burning biomass fuels are orders of magnitude higher than those found in homes in developed countries where endotoxin exposure has been linked to respiratory illness in children. There is a need for work to identify the determinants of these high concentrations, interventions to reduce exposure and health studies to examine the effects of these sustained, near-occupational levels of exposure experienced from early life.