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Background The present study was aimed to compare the effects of bilateral and unilateral bidirectional supedor cavopulmonary shunt (b-BDG and u-BDG) on pulmonary artery growth and clinical outcomes. Methods The 51 subjects enrolled in this study were divided into two groups: those receiving b-BDG (n=21) and those receiving u-BDG (n=30). Clinical records were reviewed retrospectively at a mean of 43.3 months after BDG procedures. Chi square and t-tests were performed to analyze the data. Results Left and right pulmonary artery diameters increased 27%-37% in both groups. The pulmonary artery index increased 37.2% after b-BDG and 27.0% after u-BDG b-BDG patients experienced a significant decrease in mean hemoglobin concentration and hematocrit value, and a correlated change in postoperative diameter of left pulmonary artery (LPA) and pulmonary artery index (y=0.2719, x=-1.8278; R=0.564, P=0.008). The change ratio of hemoglobin and postoperative LPA were also correlated in b-BDG patients (y=-0.0522x + 0.3539; R=-0.479, P=0.028). Only one b-BDG patient versus twelve u-BDG patients needed total cavopulmonary connections 31.8 months after BDG surgery (P=0.0074). Moreover, only one (4.8%) b-BDG patient but eight u-BDG patients (26.7%) developed pulmonary arteriovenous malformations. Conclusions b-BDG increases bilateral pulmonary blood flow and promotes growth of bilateral pulmonary arteries, with preferable physiological outcomes to u-BDG Results may imply that subsequent Fontan repair may not always be needed.