Suspected coprolites from midden, burial and room fill contexts at Çatalhöyük were analysed by GC/MS and thin section micromorphology. Assessment of sterol biomarkers enabled a distinction between faecal and non-faecal sources for the deposits to be made, with bile acid biomarkers indicating that many of the faecal deposits are human coprolites. The relative lack of ruminant faeces could be due to this material being used as a fuel source. Deposits in burials were observed to contain soil and plant derived sterols rather than their faecal counterparts. Further analysis in thin section enabled identification of associated materials and contents. Diagnostic inclusions such as bone and plant fragments were only present in some of the human coprolites, which were observed to have a very similar morphology to decayed plant remains. This study illustrates the difficulties in distinguishing coprolites in the field and under the microscope, and demonstrates the importance of integrating biogeochemical methods, particularly when such deposits are used as the basis for interpreting human health and diet, and use-of-space in settlements.