PAX8 and WT1 are transcription factors, each of them with distinct roles in organogenesis, morphogenesis, cell growth, and differentiation. Recently, their expression was also confirmed in a variety of malignancies, being included in the antibodies panel recommended for the female genital tract pathology. The aim of our study was to evaluate PAX8 and WT1 in different types of ovarian cancer (OC) with focus on (i) the completion of evidences of the Müllerian origin and (ii) the establishment of primary ovarian tumor status vs. metastasis. The study group consisted of 86 cases, with histopathological diagnosis covering the main subtypes of OC (low- and high-grade serous, low- and high-grade endometrioid, clear cell, mucinous, malignant Brenner tumor, malignant mixed Müllerian tumor, undifferentiated, and borderline). The investigation was based on immunohistochemical examination, performed by using specific antibodies applied on blocks obtained through Tissue MicroArray technique, and interpreted by scores assessing the nuclear positivity of tumoral cells. One case was not valuable due to technical difficulties. PAX8 expression was positive in 70 (81.39%) cases, the remaining 15 (17.44%) negative cases suggesting a non-Müllerian origin. WT1 expression was positive in 61 (71%) cases, mainly expressed in serous carcinoma, regardless of their differentiation degree, and negative in 24 (27%) cases. Our study provide supplementary evidences to support the association of PAX8 and WT1 immunostaining in the investigation of the complex biology of OC, PAX8 confirming the ovarian primary and WT1 allowing the refinement of the diagnosis in phenotype overlapping cases.