A variety of malignancies have been linked to major histocompatibility complex genes, including the DRB1 alleles. The association of certain DRB1 antigens with renal cell carcinoma (RCC) has been both claimed and disclaimed. To determine whether HLA-DRB1 genotypes are associated with RCC, we used the modified PCR-RFLP method for the high-resolution HLA-DRB1 genotyping of 96 Japanese RCC patients. There were no significantly frequent HLA-DRB1 alleles, whereas the DRB1*0101 and *0405 alleles had significantly lower frequencies [P = 0.004, relative risk (RR) = 0.2 and P = 0.002, RR = 0.4) in the RCC patients than in the healthy Japanese controls (n = 1216). Moreover, patients with the HLA-DRB1 *0101 or *0405 allele tended to be in earlier stages and to have less aggressive tumors than patients with neither of these alleles. The corresponding serotyping subclassification, however, showed a significantly lower frequency only for DRB1-DR1 (P = 0.01, RR = 0.3). High-resolution genotyping is essential because the polymorphism of the peptide-binding domain of major histocompatibility complex class II molecules is more precisely determined by genotypes than serotypes. In addition, inherent technical difficulties and potential typing errors render serotyping inefficient. Our data suggest that HLA-DRB1*0101 and *0405 are protective alleles for both RCC development and tumor progression.