Ovotesticular disorder is characterized by the presence of testicular and ovarian tissues in the same individual. Single gene mutations in and can lead to ovotesticular disorder of sexual development.Herein, we report a 3-month-old phenotypically female baby in whom differentiated tissues of both Müllerian and Wolffian ducts were detected on pathological analysis of laparoscopic biopsy material. Chromosomal analysis observed 46,XY, der(9)t(3;9)(p25;p24) with deletion of 9p24.3p23 including the gene cluster and duplication of 3p26.3p24.3 on array comparative genomic hybridisation.In support of previous literature, we found that haploinsufficiency of the gene cluster leads to ovotesticular disorder of sexual development. In addition, we emphasize that array comparative genomic hybridisation is an important technique in the molecular diagnosis of ovotesticular disorder of sexual.