The increased use of biomass fuel use among rural Indonesian households for years despite national program on subsidized LPG fuel distribution pose threat of indoor air pollution for the householders. Indoor air pollution levels of PM2.5 and CO in the kitchen of 40 households using the fuelwood as the main cooking fuel were measured in the same season in mountainous and coastal areas in Indonesia. The temporal variations of PM2.5 and its size distributions were simultaneously measured using photoelectric UCB monitor and personal cascade impactor, respectively. While carbon monoxide (CO) concentrations were measured using USB-CO monitors. Household indoor air pollution in the mountainous area was generally higher than that in the coastal area. This is because the households in coastal area have higher kitchen volume (about three times), smaller ventilation area (about 1.7 times) and shorter cooking duration with wood fuel (0.6 times) than those in mountainous area. Yet, during cooking with fuelwood, the indoor PM2.5 concentrations at the cook site showed almost comparable results for both sites. The wood stove burning in coastal area tended to be in flaming combustion than in mountainous area. This can be indicated by a higher fraction of finest particles in PM2.5, a higher fraction of EC in PM2.5 and a higher fraction of K+ and Cl− ions in PM2.5 mass concentrations. The time-averaged CO concentrations for 22-h measurements at the mountainous area were higher than those in coastal area. The mountainous area showed higher positive correlation relationship between the measured concentrations of CO and PM2.5 than those in the coastal area. The use of cleaner fuel, e.g., subsidized LPG fuel in rural area should be promoted and managed intensively in mountainous area than in coastal area to avoid people exposure of health damaging indoor air pollutants.