The modified Blalock-Taussig shunt (mBTS) is one of the most important palliative procedures in congenital heart surgery. However, in neonates and small infants, operative mortality and morbidity due to excessive pulmonary blood flow or shunt failure remains high. In this study, a small shunt graft (3.0-mm diameter) was estimated to determine the optimal shunt graft size of BTS as an initial palliation for ultimate biventricular circulation. Eighteen patients weighing an average 3.5 kg who underwent mBTS from July 2004 to January 2013 at our institute were reviewed. We divided the study cohort into two groups: group S (n = 10) included patients with 3.0-mm diameter shunt grafts, and group L (n = 8) included patients with 3.5-mm diameter shunt grafts. There were no hospital deaths or shunt occlusion in either group. One group L patient (12.5%) had cardiogenic shock due to excessive pulmonary blood flow. There were no differences in postoperative arterial oxygen saturation (SaO2) between the groups. There were no differences in body weight at intracardiac repair (ICR) between the groups. During the interstage to ICR, body weight gain was significantly greater in group S than in group L (P = 0.008). The small shunt graft (3.0-mm diameter) in BTS was safe, provided adequate pulmonary blood flow, and led to significant weight gain between mBTS and ICR for ultimate biventricular circulation in neonates and small infants with low body weight.