Origin of collecting duct carcinomas (CDC) of the kidney is not entirely known, although it is thought that they originate from the distal collecting duct system, whereas clear cell renal cell carcinoma (cRCC) may originate from the proximal tubular epithelium. In cRCC, the von Hippel Lindau gene (vHL) is damaged in almost 100% of cases; the frequency of vHL deletions in CDC is not known. Loss of heterozygosity (LOH) of CDC and cRCC of vHL (3p), p16 (9p), p53 (17p) and the retinoblastoma (RB) gene (13q) was studied to evaluate possible genetic differences between the two. LOH of the vHL was seen in 77.7% of cRCC and in 55% of CDC. P16 was lost in 33% of cRCC and in 50% of CDC. LOH in p53 was observed in 0/8 cases of cRCC compared to 18.7% in CDC. LOH in 13q was seen in 25% of both CDC and cRCC. The high LOH rate of the vHL gene in CDC has not been observed previously. The findings indicate that CDC and cRCC share certain genetic alterations, including frequent deletion of the vHL gene. CDC is not clearly related to cRCC but may be of heterogeneous origin.