Syndromic forms of disorders of sex development constitute a challenge for clinical and molecular investigations. We report on a 12-year-old girl presenting with lack of pubertal development, tall stature and moderate mental retardation. Conventional karyotyping at the age of 3 years revealed a male karyotype (46,XY). At the age of 12 years, the girl had no signs of puberty, and laboratory values were consistent with hypergonadotropic hypogonadism because of complete gonadal dysgenesis. Histology at the time of gonadectomy revealed fibrous tissue without testicular morphology. Cytogenetic reevaluation at that time showed additional material of unknown origin on the short arm of chromosome 9. Subsequent fluorescence in-situ hybridization and Array-CGH analyses revealed an unbalanced translocation between 9p and 15q resulting in a partial monosomy of 9p and a partial trisomy of 15q. The karyotype was described as 46,XY,der(9)t(9;15)(p23;q25.3). We discuss the clinical and molecular cytogenetic findings with respect to the literature.