Thymidylate synthase [TS, (EC 2.1.1.45)] is the target enzyme in 5-fluorouracil treatment. Recently, the DNA polymorphism of this gene has been found to affect TS protein (pTS) expression. However, no prospective studies have been performed to evaluate the influence of this polymorphism on the clinical efficacy of 5-FU-based adjuvant chemotherapy for colorectal cancer (CRC). In this study, we investigated the genotype of TS and immunopathological findings of pTS in 161 colon cancer specimens from patients who were registered in a prospective adjuvant immunochemotherapy clinical trial. The clinical course and prognosis of these patients were checked after the study had been completed. This study comprised 11 (6.8%) cases of 2R/2R, 40 (24.8%) of 2R/3R, and 110 (68.3%) of 3R/3R genotypes. All of the 2R/2R cases were still alive at the time of analysis although this finding was not statistically significant. In this prospective examination on a randomized controlled trial, the patients with colon cancer of the 2R/2R TS genotype may be good responders to 5-FU-based adjuvant chemotherapy. Furthermore, differences in the proportions of the TS genotypes can account for the interracial differences in the adverse effects of 5-FU-based chemotherapy.