Quantification of myocardial blood flow (MBF) and flow reserve has been used extensively with positron emission tomography (PET) to investigate the functional significance of coronary artery disease. Increasingly, flow quantification is being applied to investigations of microvascular dysfunction in early atherosclerosis and in nonatherosclerotic microvascular disease associated with primary and secondary cardiomyopathies. Fully three-dimensional (3D) acquisition is becoming the standard imaging mode on new equipment, bringing with it certain challenges for cardiac PET, but also the potential for MBF to be measured simultaneously with routine electrocardiography (ECG)-gated perfusion imaging. Existing 3D versus 2D comparative studies support the use of 3D cardiac PET for flow quantification, and these protocols can be translated to PET-CT, which offers a virtually noise-free attenuation correction. This technology combines the strengths of cardiac CT for evaluation of anatomy with cardiac PET for quantification of the hemodynamic impact on the myocardium. High throughput clinical imaging protocols are needed to evaluate the incremental diagnostic and prognostic value of this technology.