The expression levels of thymidylate synthase (TS) affect the sensitivity of tumor cells to fluorinated pyrimidine cytotoxic agents and determine the response of patients with colorectal cancer to fluorinated-pyrimidine-based chemotherapy. The correlation between the expression of TS and the prognosis of patients with colorectal cancer was examined in a prospective study. Evaluation of biomarkers including TS expression was performed using tumor specimens from 229 colorectal cancer patients. Immunohistochemical analysis of TS expression was performed using an antibody raised against a C-terminal epitope (D-186-V-313) of the human TS. The intensity of TS staining and the expression of other biomarkers were blindly scored. The five-year survival rates were 63.4% and 85.6% among patients with high and low intratumoral TS expressions, respectively (p=0.0007). Similarly, the disease-free survival (DFS) rate was 51.2% and 80.3% in the high and low TS expression groups, respectively (p=0.0004). In a subset analysis of Dukes' stage C patients, the survival and DFS rates were 44.0% and 40.0% in the high TS expression group, and 73.5% and 67.4% in the low TS expression group, respectively. Significant differences were observed in both survival (p=0.0048) and DFS (p=0.0054) rates. No significant correlation was observed between the expression of other biomarkers and prognosis. Significantly poorer prognosis of curatively resected colon cancer in patients with high TS expression levels in tumor tissue was confirmed by a double-blind prospective study. conducted on samples obtained from patients enrolled in an adjuvant immunochemotherapy randomized clinical trial.