The prognosis and therapy for malignant ovarian germ cell tumors including embryonal carcinoma differ from those of other categories of ovarian tumors, making accurate diagnosis imperative for patient care. Because of its rarity, the protein markers and genomic alterations typifying primary ovarian embryonal carcinoma have not been fully characterized. The present study aims to establish a set of sensitive and specific protein markers useful for the diagnosis and delineation of ovarian embryonal carcinoma. Chromosomal 12p anomalies were analyzed by dual-color fluorescence in situ hybridization. In a series of 6 ovarian mixed germ cell tumors with a component of embryonal carcinomas, OCT4, CD30, SOX2, and glypican 3 expressions were analyzed immunohistochemically on formalin-fixed paraffin-embedded tissue specimens. The results were compared to 4 cases of mixed germ cell tumor that were originally mistaken for embryonal carcinoma. OCT4 marked the nuclei of 6 cases, among which 5 cases also showed glypican 3 expression indicative of an admixed yolk sac tumor component. SOX2 was positive in only 3 cases of embryonal carcinoma. In 1 case of mixed germ cell tumor containing embryonal carcinoma, embryoid bodies from a component of polyembryoma were demonstrated to be both OCT4 and CD30 positive. Two cases originally classified as embryonal carcinoma were OCT4 and CD30 negative and showed glypican 3 positivity. They were reclassified as solid variant of yolk sac tumor. Two other cases originally classified as embryonal carcinoma were OCT4 positive and CD30 negative and were classified as immature teratoma with neuroectodermal differentiation based on the immunohistochemical findings as well as morphologic features and were diagnosed as immature teratoma. Chromosome 12p alterations were identified in 5 of 6 cases of embryonal carcinomas. In summary, a panel of immunostains is more useful than a single biomarker in the differential diagnosis of ovarian germ cell tumors. Chromosome 12p fluorescence in situ hybridization combined with OCT4, CD30, and glypican 3 immunostains is useful in confirming the diagnosis of ovarian embryonal carcinoma.