Female genital mutilation (FGM) is practiced in several areas in Iraqi Kurdistan. Cross-sectional studies of FGM provide useful detailed information to health policy makers for policy decisions and researchers to choose the appropriate interventions. However, there are some challenges in reporting FGM at ground level. This case discusses the challenges my research team and I faced in a cross-sectional survey of the prevalence of FGM in Iraqi Kurdistan. We used a multi-stage sampling technique according to the estimated population of 2017 reported by the Kurdistan Region Statistics Office to obtain the required participants in each governorate. The multi-stage random sampling technique was performed for villages in each government and households in each village. Participants’ responses were collected through a self-reported technique. The study was conducted in rural areas of three governorates: Duhok, Erbil, and Raparin. We faced challenges in reporting the prevalence of FGM that included (a) difficulty obtaining information on population and households and (b) not having an accurate list of the households from each village.