Abstract
•Primary vaginal clear cell adenocarcinoma (PVCCA) coexists with urinary tract anomalies without exposure to diethylstilbestrol in some cases.•PVCCA in our case showed genetic alterations of well-known cancer related genes, including a mutation of PIK3CA.•The genetic profile suggests that the carcinogenesis of PVCCA might have elements common with that of OCCA.