Coronary allograft vasculopathy (CAV) is a major cause of mortality in late-stage orthotopic heart transplantation (OHT) patients. Recent evidence has shown that myocardial perfusion reserve (MPR) derived from vasodilator cardiovascular magnetic resonance imaging (vCMR) and global longitudinal strain (GLS) from transthoracic echocardiography (TTE) are useful to detect CAV. However, previous studies have not comprehensively addressed whether these parameters are confounded by allograft rejection, myocardial scar/fibrosis, or allograft dysfunction. Our aim was to determine whether changes in late post-OHT MPR and GLS are due to CAV or other confounding factors. Twenty OHT patients (time from transplant to vCMR was 8.1 ± 4.1 years) and 30 controls (10 healthy volunteers and 20 with prior myocardial infarction to provide perspective with regards to the severity of any abnormalities seen in post-OHT patients) underwent vasodilator vCMR from which MPR index (MPRi), left ventricular ejection fraction (LVEF), and burden of late gadolinium enhancement (LGE) were quantified. TTE was used to measure GLS. The presence of CAV was determined from invasive coronary angiograms using thrombolysis in myocardial infarction (TIMI) frame counts and grading severity per guidelines. Previous endomyocardial biopsies were reviewed to assess association with episodes of rejection. We examined the correlations between MPRi and GLS with markers of CAV, allograft function, scar/fibrosis, and rejection. MPRi was abnormal in post-OHT patients compared to both healthy volunteers and MI controls. While there was no relationship between MPRi or GLS and LVEF, episodes of rejection, or LGE burden, both MPRi and GLS were associated with TIMI frame counts and presence and severity of CAV. Additionally, MPRi correlated with GLS (R = 0.68, P = 0.0002). In conclusion, MPRi and GLS are abnormal in late-stage OHT and associated with CAV, but not related to allograft rejection, myocardial scar/fibrosis, or allograft dysfunction. Non-invasive monitoring of MPRi and GLS may be a useful strategy to detect CAV.