Acute rejection (AR) remains the biggest challenge during the first year after heart transplantation despite advances in immunosuppressive therapy. The early detection and curbing of AR are crucial to the survival of transplant recipients. However, as the criterion standard for AR, endomyocardial biopsy has several limitations because of its inherent invasiveness and morbidity. Traditional imaging techniques, such as echocardiography and cardiac magnetic resonance imaging, are of certain value for AR, but their diagnostic criteria and accuracy remain in question. Molecular imaging sheds new light on AR diagnosis because it can provide information about gene expression and the location of molecules and cells. This article reviews the latest research and applications of several typical modalities of molecular imaging used in AR and discusses their advantages and disadvantages.