Objectives: Etiology of gonadal dysgenesis and ovotesticular syndrome is unknown in a majority of cases. To perform cytogenetic and molecular characterization of a group of patients with ovotesticular syndrome and complete gonadal dysgenesis from peripheral blood and gonadal tissue samples. Materials and methods: A total of 6 patients were included, 3 with diagnosis of 46,XX ovotesticular syndrome, one diagnosed with 46,XY ovotesticular syndrome; one with suspected 46,XX gonadal dysgenesis, and one with 46,XY complete gonadal dysgenesis. Results: All patients were evaluated with karyotype, fluorescent in situ hybridization (FISH) for SRY, multiplex ligation-dependent probe amplification (MLPA) and comparative genomic hybridization (aCGH) on peripheral blood samples. In cases with available gonadal tissue, the levels of genetic expression of SOX3, SRY, and SOX9 were determined through real-time PCR and immunofluorescence.  Rearrangements involving SRY gene were ruled out. No deletions/duplications or copy-number variations (CNV) were detected as the etiology for sexual development disorder in any of the patients studied. In a case of 46,XX ovotesticular syndrome, the gonadal karyotype was different from the karyotype in peripheral blood. Aberrant expression of SOX3 and SOX9 in gonadal tissue of a case with 46,XX ovotesticular syndrome was observed. Conclusions: Lower levels of expression of SRY and SOX9 compared to the levels in human cellular lines of embryonic testicle and Sertoli were documented in the gonadal tissue of a case with 46,XY ovotesticular syndrome. Cytogenetic and molecular studies of the gonads as a complement to peripheral blood study have the potential to enrich the understanding of sexual development disorders in patients who are XX or XY in peripheral blood.