Objectives: We aimed to determine whether epicardial and intramyocardial arteries were involved concordantly in early cardiac allograft vasculopathy. Methods: Thirty consecutive recipients who had received cardiac transplantation more than 1 year before and had a normal coronary angiogram were enrolled for intravascular ultrasound (IVUS), fractional flow reserve, coronary flow reserve and dipyridamole thallium-201 single photon emission computed tomography. Graft failure including cardiac death and retransplantation served as the primary outcome. Results: Plaque volume index and maximum area stenosis calculated from IVUS measurements correlated with coronary flow reserve deterioration in a subgroup of patients with normal fractional flow reserve (n = 13; r = –0.80, p = 0.001 and r = –0.91, p <0.0001, respectively). After follow-up for 18.4 ± 7.6 months, maximum area stenosis was found to be an independent predictor of graft failure (hazard ratio 1.43, 95% confidence interval 1.08–1.89, p = 0.012). Conclusion: In patients with physiologically normal epicardial coronary arteries, impairment of microvascular integrity correlates with the plaque burden measured by IVUS, suggesting the concordant involvement of both epicardial and resistant vessels in early cardiac allograft vasculopathy. Evident epicardial coronary narrowing on IVUS may predict graft failure in spite of normal coronary angiograms.