Background: Cardiac allograft vasculopathy (CAV) remains a major obstacle to long-term heart allograft survival. A number of studies show that immune mechanisms involved in CAV. Using non-invasive cellular MRI (CMRI) to explore indicators of CAV lesions and characterize its development could provide new insights into the target immune cells that are responsible for the progression of CAV and reveal early markers of the disease before irreversible changes occur. Methods and Results: Rat heart transplant allografts (n = 88) and isografts (n = 22) were employed in this study. CMRI at 4.7-Tesla revealed a few hypointense foci in the graft early on during CAV with more regions becoming involved as the disease progressed. The areas with hypointensity corresponded with infiltrating ED1+ cells labeled with micrometer-sized superparamagnetic iron oxide (MPIO), confirmed by MR microscopy (MRM) at 11.7-Tesla and pathology. MRI abnormalities of the transplanted hearts correlate well with the histopathological findings. MPIO-labeled cells counted by a computer algorithm that analyzed 3D MRM volumes exhibited a strong correlation with those counted by immunohistochemical inspection of ED1+ cell infiltration (R2 = 0.8075). Histology found that in the early phases of CAV, lesions were focal and mostly began in the adventitia. Immunohistochemistry indicated that the infiltrates were mostly ED1+ cells and that their density was significantly correlated with the severity of CAV (p < 0.05). Conclusions: This study illustrates the feasibility of monitoring MPIO-labeled ED1+ cells as an early indicator for CAV before vessel wall changes using non-invasive CMRI, which provides information on the entire heart.