Background The success of whole-breast radiotherapy with shorter fractionation schedules following BCS has rarely been evaluated in Japanese women. Here we present the short-term morbidity and preliminary outcomes of the shorter fractionation regimen initiated at the Kawasaki Medical School Hospital in 2003. Methods Between January 2003 and December 2005, 248 patients (251 breasts) with breast cancer underwent short-course RT following BCS. The whole breast was irradiated with a total dose of 42.5-47.8 Gy in 16-20 fractions. Patients with positive margins received additional boost irradiation to the tumor bed of 10-13.3 Gy in 4-5 fractions using 4-11 MeV electrons. Adjuvant therapy was administered in 217 cases. Results The median follow-up time was 26 months. The actuarial 4 year overall, cause specific, and disease-free survival rates were 96.7, 98.6, and 94.9%, respectively. Local recurrence was observed in one patient and distant metastases in four. The 4 year local control rate was 99.0%. A total of 221 patients developed radiation dermatitis (207 patients with grade 1, 14 patients with grade 2). The incidence of grade 2 dermatitis correlated with patient age. Radiation pneumonitis was observed in 15 patients (nine patients with grade 1, six with grade 2), two of whom developed BOOP. No difference was found in age, irradiated breast site, or use of boost irradiation, chemotherapy, and tamoxifen between those with and without pneumonitis. Conclusions The short fractionation regimen results in acceptable short-term morbidity. With limited follow-up, the incidence of recurrence in the treated breast was low.