The transporter associated with antigen processing (TAP) gene products is involved in the processing of endogenous peptides that bind to MHC class I molecules. Mutations and/or polymorphism within these genes could alter the efficacy of the immune response which might be relevant for the development of autoimmune diseases and cancer. In this study we examined both the structural integrity and the polymorphism of TAP2 in renal cell carcinoma lesions by sequencing TAP2 in renal cell carcinoma lesions and autologous normal kidney epithelium. TAP2 sequence analysis of 31 renal cell carcinoma lesions, one oncocytoma and respective autologous normal kidney epithelium revealed no mutation in the TAP2 gene, whereas a TAP2 polymorphism was detected at position -36 up-stream of the ATG. This polymorphism is heterozygous in about 66% of the lesions analyzed. In addition, heterozygosity at base pair position 1797 downstream of the ATG was found, which did not affect the amino acid composition. The distribution of the TAP2 alleles analyzed in the different lesions demonstrated a 48.4% homozygosity of the tumors regarding different N-SNPs. Most of the known S-SNPs showed 61.3% heterozygosity independent of a particular allele. Thus, TAP2 gene polymorphism is not linked to renal cell carcinoma since no association between a particular amino acid residue and the disease was found.