The diagnosis of metastatic clear cell renal cell carcinoma (CC-RCC) can be difficult because of its morphologic heterogeneity and the increasing use of small image-guided biopsies that yield scant diagnostic material. This is further complicated by the degree of morphologic and immunophenotypic overlap with non-renal neoplasms and tissues, such as adrenal cortex. In this study, a detailed immunoprofile of 63 adrenal cortical lesions, which included 54 cortical neoplasms, was compared with 185 metastatic CC-RCC using traditional [anti-calretinin, CD10, anti-chromogranin, anti-EMA, anti-inhibin, anti-melanA, anti-cytokeratins (AE1/AE3 and AE1/CAM5.2), anti-renal cell carcinoma marker (RCCma), and anti-synaptophysin)] and novel [anti-carbonic anhydrase-IX (CAIX), anti-hepatocyte nuclear factor-1b (HNF-1b), anti-human kidney injury molecule-1 (hKIM-1), anti-PAX-2, anti-PAX-8, anti-steroidogenic factor-1 (SF-1), and anti-T cell immunoglobulin mucin-1 (TIM-1)] antibodies. Tissue microarray methodology was used to simulate small image-guided biopsies. Staining extent and intensity were scored semiquantitatively for each antibody. In comparing different intensity thresholds required for a ‘‘positive’’ result, ≥2+ was identified as optimal for diagnostic sensitivity/specificity. For the distinction of adrenal cortical lesions from metastatic CC-RCC, immunoreactivity for the adrenal cortical antigens SF-1 (86% adrenal; 0% CC-RCC), calretinin (89% adrenal; 10% CC-RCC), inhibin (86% adrenal; 9% CC-RCC), and melanA (86% adrenal; 10% CC-RCC) and the renal epithelial antigens hKIM-1 (0% adrenal; 83% CC-RCC), PAX-8 (0% adrenal; 83% CC-RCC), HNF-1b (0% adrenal; 76% CC-RCC), EMA (0% adrenal; 78% CC-RCC), and CAIX (3% adrenal; 87% CC-RCC) had the most potential utility. The use of the novel renal epithelial markers hKIM-1 (clone AKG7) and/or PAX-8, and the adrenocortical marker SF-1 in an immunohistochemical panel for distinguishing adrenal cortical lesions from metastatic CC-RCC offers improved diagnostic sensitivity and specificity.