True hermaphroditism (TH) refers to individuals who have both unequivocal ovarian tissue and testicular elements regardless of their karyotypes; whereas mixed gonadal dysgenesis (MGD) refers to individuals who usually have a differentiated gonad on one side and a streak gonad or streak testis on the other side. A differential diagnosis between the TH and MGD has important clinical implications for gender assignment and the decision for early gonadectomy; however, variable clinical and histological features frequently lead to the confusion of TH with MGD. We reviewed the clinicopathological features of TH (n = 4) and MGD (n = 6) in young children to identify which morphological features are important for a differential diagnosis between the two conditions. In both conditions, the testicular compartment was composed of immature seminiferous tubules lined by immature Sertoli cells and primitive germ cells; this finding was not helpful for a differential diagnosis. The ovarian compartment in TH cases showed numerous primordial follicles containing primary oocytes with a few primary or antral follicles; however, ovarian compartments in patients with MGD were characterized by primitive sex-cordlike structures with or without germ cell components within the ovarian-type stroma, mimicking gonadoblastomas in two cases and granulosa cell or Sertoli cell tumors in three cases. Hormonal profiles, cytogenetic results, and an internal duct system were not helpful in a differential diagnosis. In conclusion, a differential diagnosis between TH and MGD is largely dependent on the histological features of the gonads. Therefore, examination of all resected or biopsied tissue and the application of strict histological criteria are important.