The biology of renal cell carcinoma (RCC) remains poorly understood. RCC, which accounts for up to 3% of all adult malignancies, is the most common neoplasm in the adult kidney and has been increasing in incidence. These tumors are classified into five main subtypes: clear cell, papillary, and chromophobe RCC, as well as collecting duct carcinoma and oncocytoma. Of these, clear cell and papillary are the two most frequently diagnosed subtypes and both arise from the proximal tube of the kidney. Despite sharing a common origin, they are histologically and genetically distinguishable and thus represent an optimal model system for studying tumor-specific and tumor-subtype specific expression patterns. The aim of this study was to identify potential marker genes for clear cell and papillary RCC, assess their specificity and relevance for the tumor-subtypes, and thus contribute to a better characterization of the tumor development and behavior of RCC. To address these questions, this study combined translational and transcriptional approaches to analyze the protein and gene expression of both tumor subtypes.