Recent studies have demonstrated that a detailed knowledge of the extent of angiographic coronary artery disease (CAD) is not a prerequisite for clinical decision making, and the clinical management of patients with CAD is more and more focused towards the identification of myocardial ischemia and the quantification of ischemic burden. In this view, non-invasive assessment of ischemia and in particular stress imaging techniques are emerging as preferred and non-invasive options. A quantitative assessment of regional myocardial perfusion can provide an objective estimate of the severity of myocardial injury and may help clinicians to discriminate regions of the heart that are at increased risk for myocardial infarction. Positron emission tomography (PET) has established itself as the reference standard for myocardial blood flow (MBF) and myocardial perfusion reserve (MPR) quantification. Cardiac magnetic resonance (CMR) is increasingly used to measure MBF and MPR by means of first-pass signals, with a well-defined diagnostic performance and prognostic value. The aim of this article is to review the currently available evidence on the use of both PET and CMR for quantification of MPR, with particular attention to the studies that directly compared these two diagnostic methods.