Background: The purpose of this study was to evaluate rate of pathologic complete response (pCR) in patients with locally advanced rectal cancer treated with neoadjuvant chemoradiotherapy (CRT) with 5-FU/leucovorin (FL) versus Irinotecan/S-1 (IS) and surgery followed by fluoropyrimidine based adjuvant chemotherapy. Methods: Patients with resectable, locally advanced (cT3-4 and/or cN positive) adenocarcinoma of rectum were randomly assigned to receive preoperative radiation (45-50.4 Gy in 25-28 daily fractions) and concomitant chemotherapy with bolus injections of 5-FU 400 mg/m²/day and LV 20 mg/m²/day for 3 consecutive days every 4 weeks for 2 cycles (FL group), or with irinotecan 40 mg/m² on days 1, 8, 15, 22, 29 and S-1 35mg/m² twice on the day of irradiation (Monday-Friday) (IS group). Curative surgery was performed for about 4-8 weeks after the completion of chemoradiotherapy. Postoperative chemotherapy regimen is FL. The primary endpoint was pCR rate. Results: 142 eligible patients were randomly assigned. Of 142, 130 patients (91.5%) underwent total mesorectal excision. The pCR was achieved 11 (17.2 %) of 64 patients in the FL group and was 16 (24.2%) of 66 patients in the IS group (p=0.1). When pCR was combined with few residual cells, the rate was significantly higher in IS group compared to FL group (57.6 % vs. 39.1 %, p-value=0.035). Preoperative rate of grade 3-4 toxicity was 1.4% with FL and 7.0 % with IS group (p=0.095). Conclusions: The results have suggested that neoadjuvant CRT using IS is feasible and effective for patients with locally advanced rectal cancer. Longer follow-up is needed to assess survival. Clinical trial information: NCT01269216.