A cDNA isolated by a subtractive hybridization procedure detected loss of mtDNA and the mRNA coding for NADH dehydrogenase subunit 3 in 8 of 13 tumor kidney tissues obtained from patients with renal cell carcinoma. Sequencing revealed a stretch of nucleotides homologous to the mitochondrial NADH dehydrogenase subunit 3 gene in the middle of the cDNA. The depletion phenomenon was also observed in five of six renal carcinoma cell lines. In the case of a benign renal oncocytoma, however, the mtDNA content was increased 200% more than that of the adjacent normal tissue. The frequency with which this phenomenon occurs in renal cell carcinomas, but not in other types of cancers, suggests that this may be an important phenotype associated with renal cell neoplastic transformation. However, the absence of any structural alterations within the mitochondrial genome suggests that the depletion may be a secondary event associated with the oncogenic transformation process.