Ovarian tumors containing cells with transitional cell morphology are recognized in the 1999 World Health Organization classification of ovarian tumors and include benign Brenner tumor, borderline and malignant Brenner tumor, and transitional cell carcinoma. Recent immunohistochemical investigations have reached conflicting conclusions regarding true urothelial differentiation in ovarian Brenner tumors. We evaluated a panel consisting of antibodies to uroplakin III (UROIII), thrombomodulin (THR), cytokeratin 7 (CK7), cytokeratin 20 (CK20), and Wilms' tumor protein (WT1) to study urothelial differentiation in ovarian transitional cell tumors. Additionally, we compared the immunohistochemical profile of transitional cell carcinoma of the ovary (TCC-O) with that of transitional cell carcinoma of the bladder (TCC-B), to ascertain if immunohistochemistry may aid in distinguishing primary from metastatic TCC-O. Seventeen benign Brenner tumors and 17 TCC-O were stained with antibodies to UROIII, THR, CK7, CK20, and WT1. Additionally, 6 Brenner tumors of borderline malignancy were stained with antibodies to UROIII, THR, CK7, and CK20. The immunohistochemical results were compared with those of 30 cases of noninvasive TCC-B (low malignant potential n=14, low grade n=16) and 36 cases of invasive TCC-B stained with a similar panel of antibodies as part of another study. Twenty-one nontransitional cell ovarian carcinomas (9 serous, 4 clear cell, 5 endometrioid, 2 mixed endometrioid/serous, and 1 mucinous) were used as controls. Most Brenner tumors showed positivity with UROIII (82%) and THR (76%), supporting true urothelial differentiation in these tumors. Although TCC-O has considerable morphologic overlap with TCC-B, they had only partial immunophenotypic overlap. TCC-O rarely expressed UROIII (6%) and THR (18%) and none expressed CK20. In contrast, nearly 40% of invasive TCC-B expressed UROIII, 61% expressed THR, and 50% expressed CK20. Nearly 82% of TCC-O expressed WT1, which was negative in all TCC-B. Our results may have diagnostic value in distinguishing TCC-O (CK20-, UROIII-/+, WT1+) and invasive TCC-B (CK20+, UROIII+/-, WT1-) metastatic to the ovary. They also indicate that the morphologic similarity between TCC-O and TCC-B does not indicate any histogenic similarity and, as others have noted, TCC-O is a variant morphology in the spectrum of surface epithelial carcinomas.