Fontan patients are at risk for hepatic fibrosis; however, risk factors are unclear. We performed a multivariate analysis in a small cohort of 14 patients (7–24 years old, mean 15) with Fontan circulation, undergoing cardiac catheterization and transvenous liver biopsies, all demonstrating fibrosis. We found by stepwise regression analysis that the history of pulmonary atresia was a predictor of higher total hepatic fibrosis scores than a history of unobstructed pulmonary blood flow (p = 0.002). Other variables including age, time from Fontan, hemodynamic measurements, and laboratory values were not predictive of total fibrosis scores at p values <0.05. Hepatic fibrosis scores between those born with pulmonary atresia versus unrestricted pulmonary blood flow may reflect differences in pulmonary circulatory physiology, resulting from differences in pulmonary vascular development.