The dominant ventricular morphology affects both the early and late outcomes of the Fontan procedure, but its impact on the patients' status immediately following the Glenn procedure is unknown. This study aims to evaluate the effect of the infants' dominant ventricular morphology on the immediate course after undergoing the Glenn procedure. This single-center, retrospective study included all patients who underwent the Glenn procedure between October 2003 and May 2016. The patients were divided into two groups according to their dominant ventricular morphology. Their postoperative records were reviewed and compared. Out of the 89 patients who underwent the Glenn procedure during the study period, 40 (44.9%) had dominant right ventricular morphology and 49 (55.1%) had left ventricular morphology. There were no significant group differences in baseline characteristics or operative data. The maximal postoperative vasoactive-inotropic score was significantly higher and the extent of ventricular dysfunction was significantly more severe in the dominant right ventricle group (P < 0.05). The length of hospitalization was slightly but not significantly longer in the hypoplastic LV group. It is concluded that patients with a dominant LV morphology had a superior ventricular function and required less inotropic support compared to that of a dominant RV morphology in the immediate postoperative course following the Glenn procedure. Survival was not affected by these differences. Further study to determine the pathophysiologic basis for these differences is warranted.