Dihydropyrimidine dehydrogenase (DPD) is the enzyme catalyzing the first step of pyrimidine metabolism. To date, genetic polymorphisms of pyrimidine-synthesizing enzymes have been reported to be associated with the risk of malignant lymphoma or colon cancer. Accordingly, there may be associations between dihydropyrimidine dehydrogenase (DPYD) polymorphism and the risk of malignancies. We conducted a prevalent case-control study to investigate the associations between a functional polymorphism of dihydropyrimidine dehydrogenase, DPYD T85C, and the risk of six malignancies. Controls were 445 Nagoya City inhabitants without a history of malignancy who had participated in a health check-up between August and September 2000. Case subjects were 901 patients with malignancies (99 esophageal, 131 gastric, 143 colon, 179 lung, 243 breast, and 106 malignant lymphomas) who had visited Aichi Cancer Center Hospital between March 1999 and December 2000. No DPYD CC individuals were found in either cases or controls. The frequency of DPYD TC genotype was 6.3% in control subjects and 5.9% in all case subjects (not significant). In a subgroup analysis, the frequency of TC genotype was highest in patients with gastric cancer (9.1%), followed by those with lung cancer (8.3%), with the lowest frequency in those with malignant lymphoma (1.9%). The gender- and age- adjusted odds ratios and 95% confidence intervals for the TC genotype of gastric cancer and malignant lymphoma were 1.52 (0.71-3.28) and 0.31 (0.71-1.34), respectively. Although prevalent cases were used, this study suggested that the influence of DPYD T85C posed only a limited risk for the six malignancies.