Connexin 43 (Cx43) forms gap junction channels that are essential for the propagation of electrical depolarization in cardiomyocytes, but also with important roles in the pathophysiology of reperfusion injury. However, more recent studies have shown that Cx43 has also important functions independent from intercellular communication between adjacent cardiomyocytes. Some of these actions have been related to the presence of Cx43 in the mitochondria of these cells (mitoCx43). The functions of mitoCx43 have not been completely elucidated, but there is strong evidence indicating that mitoCx43 modulates mitochondrial respiration at respiratory complex I, production of radical oxygen species and ATP synthesis. These functions of mitoCx43 modulate mitochondrial and cellular tolerance to reperfusion after prolonged ischemia and are necessary for the cardioprotective effect of ischemic preconditioning. In the present review article we discuss available knowledge on these functions of mitoCx43 in relation to reperfusion injury, the molecular mechanisms involved and explore the possibility that mitoCx43 may constitute a new pharmacological target in patients with ST-segment elevation myocardial infarction (STEMI). This article is part of a Special Issue entitled: Gap Junction Proteins edited by Jean Claude Herve.