Background: Female genital mutilation/Cutting (FGM/C) can result in short and long-term complications, which can impact physical, psychological and sexual health. Our objective was to obtain descriptive data about the most frequent health conditions and procedures associated with FGM/C in Swiss university hospitals inpatient women and girls with a diagnosis of FGM/C. Our research focused on the gynaecology and obstetrics departments. Methods: We conducted an exploratory descriptive study to identify the health outcomes of women and girls with a coded FGM/C diagnose who had been admitted to Swiss university hospitals between 2016 and 2018. Four of the five Swiss university hospitals provided anonymized data on primary and secondary diagnoses coded with the International Classification of Diseases (ICD) and interventions coded in their medical files. Results: Between 2016 and 2018, 207 inpatients had a diagnosis of FGM/C. The majority (96%) were admitted either to gynaecology or obstetrics divisions with few genito-urinary and psychosexual conditions coded.Conclusions: FGM/C coding capacities in Swiss university hospitals are low, and some complications of FGM/C are probably not diagnosed. Pregnancy and delivery represent key moments to identify and offer medical care to women and girls who live with FGM/C. Trial registration: This cross-sectional study (protocol number 2018-01851) was conducted in 2019, and approved by the Swiss ethics committee.