Renal tumors are classified by light microscopy using the World Health Organization (WHO) system. Recently, WHO system defines histopathologic tumor subtypes with distinct clinical behavior and underlying genetic alterations. In adults, the vast majority of renal carcinomas are variants of renal cell carcinoma (RCC). Histopathologic classification is critical for determining the prognosis and clinical management of RCC. Since the recognition of novel tumor subtypes, and development of procedures yielding small diagnostic biopsies, gene expression studies came to insight besides immunohistochemistry. Gene expression profile studies also provided new markers that identify patients with a poor prognosis as well as identifying potential therapeutic targets. Therefore, classification systems based on gene expression are likely to become essential for diagnosis, prognosis and treatment of renal carcinomas. DNA micro-array studies have shown that clinically relevant renal tumor subtypes are characterized by distinct gene expression profiles, which are useful for discovery of novel diagnostic and prognostic bio-markers. Although strict criteria are not possible to classify each case according to its gene profile, renal tumors are one of the best candidates that molecular classification would be applied in a good correlation with clinical behavior and prognosis. Micro-array studies have advanced our knowledge of renal tumor pathogenesis, prognosis and therapy.