This review describes methodologies used to study experimental myocardial ischemic and reperfusion injury. Myocardial reperfusion injury may be manifest as myocardial stunning, ventricular arrhythmias, coronary vascular dysfunction, or the extension of the area of myocyte necrosis beyond that due to the ischemic insult alone. This review discusses methodology pertaining to the latter form of reperfusion injury. The pathophysiology of the reperfusion injury process is complex, including primarily cellular and humoral components of inflammation, as well as myocellular ionic and metabolic disturbances. Since the extent of injury may be influenced by methodological considerations this review aims to discuss the principle means of characterizing reperfusion injury in the experimental setting. The methods discussed are principally those related to in vivo research. Where appropriate, advantages, disadvantages, or alternate methods will be presented. Lastly, as understanding of the pathophysiology of reperfusion injury increases, newer techniques utilizing murine models, the study of apoptotic cell death, and the role of gender may be used more frequently and are thus briefly reviewed.