Objectives To investigate the accuracy of assigned diagnosis in XY female intersex conditions.Design Cross sectional hospital case notes review.Setting Tertiary hospital multidisciplinary intersex clinic.Sample Forty-six adult intersex women with a complete or mosaic XY karyotype.Methods All clinical features and investigation results were reviewed and a diagnosis was assigned. This was compared to the original diagnosis assigned. Main outcome measures Data collected included presentation, all investigations, subsequent clinical course and all treatments (medical and surgical). These data were employed to assign an up-to-date intersex diagnosis, which was compared with the recorded diagnosis in the hospital case notes. Diagnoses were then rated according to level of accuracy. Results The 47.8% patients had an accurate diagnosis, 32.6% of diagnoses were inaccurate and currently under review, 13% had a wrong diagnosis and 6.5% remain with an unknown aetiology for their XY intersex condition. Conclusions Diagnostic accuracy is assumed to be high when evaluating published work on these conditions; however, this study shows 52.1% of patients have unknown, inaccurate or wrong diagnoses. Assigning the wrong diagnosis may be harmful, for example, if it leads to irreversible virilising changes or development of a gonadal malignancy, and for all cases excludes accurate condition management and genetic counselling for both the patient and their immediate family.