Solid fuel combustion is an important risk factor of morbidity. This study was conducted to determine the effect of indoor air pollution (IAP) due to solid fuel combustion on physical growth in 262 Sri Lankan children under five. Exposure was defined by the type of fuel used for cooking. Pollutant levels were measured in a subsample of households. "High" exposure group (households using biomass fuel/kerosene oil for cooking) comprised 60% of the study population; the prevalence of wasting was 19.7% and underweight was 20.4% in the entire population where 68% were from the high exposure group. Children from the "high" exposure group had significantly lower mean z-scores for weight-for-height (p = 0.047), height-for-age (p = 0.004) and weight-for-age (p = 0.001) as compared to the "low" exposure group (children of households using liquefied petroleum gas and/or electricity) after adjusting for confounders. Z-scores of weight-for-age, height-for-age and weight-for-height were negatively correlated with CO (p = 0.001, 0.018, 0.020, respectively) and PM2.5 concentrations (p<0.001,p = 0.024 p = 0.008, respectively). IAP due to combustion of biomass fuel leads to poor physical growth.