We investigated the endothelial function in MELAS patients and also evaluated the therapeutic effects of L-arginine. Concentrations of L-arginine during the acute phase of MELAS were significantly lower than in control subjects. L-arginine infusions significantly improved all symptoms suggesting stroke within 30 min, and oral administration significantly decreased frequency and severity of stroke-like episodes. Flow-mediated dilation (FMD) in patients showed a significant decrease than those in the controls. Two years of oral supplementation of L-arginine significantly improved endothelial function to the control levels and was harmonized with the normalized plasma levels of L-arginine in patients. L-arginine therapy showed promise in treating stroke-like episodes in MELAS.