In locally advanced rectal cancer, neoadjuvant 5-fluorouracil (5-FU)-based long-term chemoradiotherapy leads to marked tumor reduction and decrease of local recurrence rate. Thymidylate synthase (TS), thymidine phosphorylase (TP), and dihydropyrimidine dehydrogenase (DPD) are known to be important biomarkers to predict tumor response to 5-FU-based therapy. The aim of this study was to examine the correlation between TS, TP, and DPD protein expression and histopathologic tumor regression after neoadjuvant chemoradiotherapy. The results were compared with the recently published mRNA data. Preoperative biopsies (n = 25) and resection specimens (n = 40) from patients with rectal carcinoma (clinical UICC stage II/III) receiving neoadjuvant 5-FU-based chemoradiotherapy were studied for TS, TP, and DPD protein expression by immunohistochemistry using three different scoring systems (intensity, pattern, intensity + pattern). Results were compared with histopathologic tumor regression. A significant correlation between protein expression and tumor response was only seen when both staining intensity and staining pattern were considered. With this method, a significant association was seen between high TS expression in tumor biopsies as well as resection specimens and nonresponse of the tumor to therapy (P = 0.04). Furthermore, low TP expression in the resection specimens was significantly associated with lack of response (P = 0.02). For DPD no significant correlations were found at all. In conclusion, these results suggest that immunohistochemistry like RT-PCR is a suitable method to determine the correlation between TS, TP, and DPD expression and histopathologic tumor regression. However, precise results can only be achieved if staining intensity as well as staining pattern within the tumors are evaluated.