To identify new tumor specific proteins of renal cell carcinoma (RCC) using proteomic analysis. Nine renal cell carcinomas were resected and these surgical operations were carried out from June 2007 to September 2008 in the Urology Department of the Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China. The cancer tissues and para-cancer normal tissues were preserved in liquid nitrogen. We analyzed the RCC tissues and para-cancer normal tissues by 2-dimensional polyacrylamide gel electrophoresis (2D-PAGE). The 16 differentially expressed protein spots (p<0.05 by Student t-test) were identified by matrix assisted laser desorption ionization/time of flight mass spectrometry and tandem mass spectrometry. Six proteins were down regulated and 10 proteins were up regulated in clear cell RCC compared with corresponding normal kidney tissue. The down regulated proteins were calbindin, ester hydrolase C11orf54, alcohol dehydrogenase, ammecr1-like protein, adenosine diphosphate (ADP)/adenosine-5'-triphosphate (ATP) translocase 3 and leucine-tyrosine-arginine (LYR) motif-containing protein 5. The up regulated proteins were hypoxia inducible domain family member 1A, glutathione S-transferase P, thioredoxin-dependent peroxide reductase, peroxiredoxin-6, CD2-associated protein, annexin A5, gamma-enolase, retinal dehydrogenase 1, vimentin, and protein-glutamine gamma-glutamyltransferase 2. The data provide potential tumor markers for diagnosis of RCC.