Malignancy developing in extragonadal endometriosis is rare with the majority of cases being endometrioid adenocarcinomas. We present a 54-year-old woman who developed a clear cell carcinoma in her perineum, 25 years after excision of a perineal endometrioma in an episiotomy scar. Treatment involved radiotherapy and surgery, with a view to preserving vaginal function. Where benign extragonadal endometriosis occurs, the potential for malignant transformation persists even years after primary treatment.