Disorders of sex development (DSD) are defined as congenital conditions associated with atypical development of chromosomal, gonadal or phenotypical sex. Majority of 46XY DSD patients present clinical characteristics of primary amenorrhea. However few cases with secondary amenorrhea are reported in the literature. It was suggested that such patients might have an estrogen secretion by a tumoral lesion. In other cases, it could be a misdiagnosed 46,XY DSD following bone marrow transplantation. We report here the third case of misdiagnosed 46,XY DSD following bone marrow transplantation. Our patient is a 15-year old girl referred to our department of endocrinology for secondary amenorrhea. She had been diagnosed with lymphoblastic Leukemia at the age of 13. She received chemotherapy and total body irradiation after which she had bone marrow transplantation. The hormonal profile confirmed the primary ovarian insufficiency. Chromosomal analysis performed on peripheral blood lymphocytes showed a 46,XY karyotype consisting with a diagnosis of 46, XYDSD. However, regarding her past medical history, we complete with karyotype on skin fibroblasts that showed a normal female karyotype. Thus we conclude that our patient had a misdiagnosed 46,XYDSD, and that her secondary amenorrhea is caused by chemotherapy and radiotherapy. The fertility prognosis is considered poor in that case. Although the need for fertility preservation has to be weighed against morbidity and mortality associated with cancer, our findings highlight the importance of fertility preservation by oocyte and/or embryo cryopreservation for such patients.