The use of wood, dung and other biomass fuels can be traced back to early prehistory. While the study of prehistoric fuel use and its environmental impacts is well established, there has been little investigation of the health impacts this would have had, particularly in the Neolithic period, when people went from living in relatively small groups, to living in dense settlements. The UNESCO World Heritage Site of Çatalhöyük, Turkey, is one of the earliest large ‘pre-urban’ settlements in the world. In 2017, a series of experiments were conducted to measure fine particulate (PM2.5) concentrations during typical fuel burning activities, using wood and dung fuel. The results indicate that emissions from both fuels surpassed the WHO and EU standard limits for indoor air quality, with dung fuel being the highest contributor for PM2.5 pollution inside the house, producing maximum values > 150,000 µg m−3. Maximum levels from wood burning were 36,000 µg m−3. Average values over a 2–3 h period were 13–60,000 µg m−3 for dung and 10–45,000 µg m−3 for wood. The structure of the house, lack of ventilation and design of the oven and hearth influenced the air quality inside the house. These observations have implications for understanding the relationship between health and the built environment in the past.