Objective To compare acute toxicity for stage Ⅱ-Ⅲ patients with rectal cancer irradiated with helical tomotherapy (HT) and conventional five-field intensity-modulated radiotherapy (5-IMRT). Methods The data of 84 stage Ⅱ-Ⅲ patients with rectal adenocarcinoma treated with concurrent chemoradiotherapy (CRT) were retrospectively analyzed. 19 patients underwent postoperative CRT, and 65 patients underwent preoperative CRT. 43 patients received radiotherapy with HT and 41 patients with 5-IMRT. The delineation on clinical target volume (CTV) and gross tumor target (GTV) was similar for two groups. The CTV to plan tumor volume (PTV) margins were 1.0 cm for patients with 5-IMRT and 0.5 cm for patients with HT. For all patients, a dose of 45.0-50.4 Gy, in daily fractions of 1.8 Gy, was delivered to PTV. For 45 patients with high risk factors, simultaneous integrated boost (SIB) was given to the tumor or tumor bed of a total dose of 55.0-60.0 Gy, in daily fractions of 2.1-2.3 Gy. Before treatment, the patients treated with HT underwent scanning by the tomotherapy-integrated megavoltage computed tomography (MVCT) scan modality and were positioned by co-registration of these images to the original kilovoltage planning CT image set. Concurrent capecitabine every day 1 600 mg/m2, twice daily on every day in the week. Results The rates of grade ≥2 acute cystitis were 7.0 % (3 cases) in HT group and 2.4 % (1 case) in 5-IMRT group (P= 0.616), and ≥3 grade acute diarrhea were 4.7 % (2 cases) and 12.2 % (5 cases), respectively (P= 0.259). ≥2 grade leukopenia were 48.8 % (21 cases) and 19.5 % (8 cases), respectively (P= 0.005), ≥1 grade anemia were 34.9 % (15 cases) and 14.6 % (6 cases), respectively (P= 0.032), and ≥1 grade thrombocytopenia were 23.3 % (10 cases) and 14.6 % (6 cases), respectively (P= 0.314). Conclusions There is no significant difference in acute diarrhea and cystitis for patients treated with HT and 5-IMRT. Leukopenia and anemia in patients treated with HT are worse than those in patients with 5-IMRT, and thrombocytopenia is similar in the two groups. Key words: Rectal neoplasms; Chemoradiotherapy; Helical tomotherapy; Acute toxicity