The relation between underlying ventricular morphology and regional function in patients with Fontan circulation remains unclear. The aim of this study was to compare regional function and its heterogeneity in patients with tricuspid atresia (TA), biventricular apex-forming morphology (BiV), and controls. Nineteen patients (median age 12 years) with Fontan circulation who presented consecutively were prospectively enrolled and compared with age- and heart rate–matched controls. Most patients were in New York Heart Association class I (63%). Longitudinal systolic strain (S), systolic strain rate (SR_sys), and early diastolic strain rate (SR_dia) peaks were obtained from 6 ventricular segments, and a coefficient of variation by segment was calculated as a measure of regional heterogeneity. Systolic S, SR_sys and SR_dia peaks were decreased at the right and left lateral walls in both patient groups compared with controls (p ≤0.001 for all). Patients with TA had higher systolic S and SR_sys in the middle of the right lateral wall than those with BiV morphology (p = 0.009 and p = 0.001, respectively). The mean coefficients of variation assessed by S and SR_sys were similar in controls and patients with TA but lower in those with BiV than in controls and patients with TA (p <0.001 and p = 0.01, respectively). The mean coefficient of variation assessed by SR_dia was greater only in patients with BiV than in controls (p = 0.001). In conclusion, patients with Fontan circulation have more heterogenous systolic and early diastolic regional function than healthy control subjects, and patients with TA have better systolic regional function in the middle of the right lateral wall and less systolic heterogeneity than patients with BiV morphology.