The objective of this study was to compare histopathological changes in hypoplastic left heart syndrome right ventricles (RV) of patients undergoing Sano and modified Blalock–Taussig (MBT) shunt and correlate them with echocardiographic findings. Myocardial tissue samples were obtained from hearts with Sano or MBT shunts after transplantation or at autopsy. Histologic sections were reviewed manually and by automated digital image analysis. Velocity vector imaging was performed on echocardiogram images obtained before transplant or death. All of these parameters were compared between the Sano and MBT shunt cohorts. A total of 14 specimens (7 Sano and 7 MBT shunt) were studied. Median age at transplant/death of Sano and MBT shunt cohorts was 11 (range 2–41) and 8 months (range 2–200), respectively. All Sano specimens had a scar at ventriculotomy site, and the mean scar area was 6.2 ± 3.3 cm². Compared with remote RV free wall, myocardium bordering the scar showed increased fibrosis (34 ± 16 % vs. 28 ± 14 %, p = 0.04) and thinning (0.8 ± 0.9 vs. 5.3 ± 0.8 mm; p < 0.001), which did not regress with time. The Sano ventriculotomy site showed significantly decreased velocity, strain, and strain rate compared with the corresponding contralateral segment. No focal scarring or regional hypokinesia was seen in the MBT shunt cohort. This is the first study to demonstrate histopathological features of ventriculotomy-associated RV myocardial scarring and myocardial thinning. The scarred ventriculotomy site showed decreased segmental myocardial deformation after Norwood with Sano shunt.