Variety of ion channels is present in plasma membrane of endothelial cells. These include the potassium channels such as Ca(2+)-activated K(+) channels, inwardly rectifying K(+) channels, voltage-dependent K(+) channels and also ATP-regulated K(+) channels. Due to an influence on the membrane potential they are important regulators of vascular tone by modulating endothelial calcium ions signaling and synthesis of vasodilating factors. Potassium channels in mitochondrial membranes of various tissues, similar to plasma membrane potassium channels, are described. Mitochondrial potassium channels such as ATP-regulated or large conductance Ca(2+)-activated and voltage gated channels are implicated in cytoprotective phenomenon in different tissues. In this paper we describe the pharmacological properties of mitochondrial potassium channels and discuss their role of as novel pharmacotherapeutic targets in endothelium.