In this review we have examined the role of perfusion CMR for evaluating the integrity and function of the microcirculation. We have discussed the techniques for fully quantifying myocardial blood flow and the impact of different imaging parameters on quantification. Perfusion CMR not only identifies the presence of microvascular obstruction after a myocardial infarction but also relates it to patient prognosis. The ability to absolutely quantify myocardial blood flow improves the detection and evaluation of epicardial coronary disease and its risk factors. CMR perfusion imaging has proved to be an invaluable tool for understanding the integral role of the microcirculation in a variety of other cardiac disorders. Another advantage of perfusion CMR is the ability to measure differences in subendocardial and subepicardial blood flow. Newer techniques such as ASL and BOLD imaging promise to further improve the ability of CMR to assess the microcirculation without the use of exogenous contrast agents.