Intravascular ultrasound (IVUS)-based reconstructions have been traditionally used to examine the effect of endothelial shear stress (ESS) on neointimal formation. The aim of this analysis is to compare the association between ESS and neointimal thickness (NT) in models obtained by the fusion of optical coherence tomography (OCT) and coronary angiography and in the reconstructions derived by the integration of IVUS and coronary angiography. We analyzed data from six patients implanted with an Absorb bioresorbable vascular scaffold that had biplane angiography, IVUS and OCT investigation at baseline and 6 or 12 months follow-up. The IVUS and OCT follow-up data were fused separately with the angiographic data to reconstruct the luminal morphology at baseline and follow-up. Blood flow simulation was performed on the baseline reconstructions and the ESS was related to NT. In the OCT-based reconstructions the ESS were lower compared to the IVUS-based models (1.29 ± 0.66 vs. 1.87 ± 0.66 Pa, P = 0.030). An inverse correlation was noted between the logarithmic transformed ESS and the measured NT in all the OCT-based models which was higher than the correlation reported in five of the six IVUS-derived models (−0.52 ± 0.19 Pa vs. −0.10 ± 0.04, P = 0.028). Fusion of OCT and coronary angiography appears superior to IVUS-based reconstructions; therefore it should be the method of choice for the study of the effect of the ESS on neointimal proliferation.