Immunohistochemistry may be a very useful adjunct to morphologic diagnosis in many areas of surgical pathology, including genitourinary pathology. In this review, we address common diagnostic dilemmas where immunophenotypic analysis may be utilized and we highlight pitfalls specific to each scenario. For prostate, we review the diagnosis of limited prostatic adenocarcinoma and the distinction of high-grade prostatic adenocarcinoma from urothelial carcinoma. We also cover markers of urothelial lineage in the diagnosis of metastatic carcinoma of unknown primary site. In the kidney, distinction of poorly differentiated renal cell carcinoma from urothelial carcinoma and epithelioid angiomyolipoma, adjuncts to the recognition of hereditary renal neoplasia, and the diagnosis of metastatic renal cell carcinoma are discussed. Finally, for testis we address distinction of germ cell tumors from sex cord-stromal tumors, as well as the diagnosis of metastatic germ cell tumors.