Peroxynitrite (ONOO−) is a powerful oxidant produced from the reaction of nitric oxide (NO) and superoxide (O2˙−). In healthy cells, a balance exists between endogenous antioxidants and pro-oxidants to prevent oxidation, nitrosation, and nitration reactions with cellular macromolecules, and reactions of peroxynitrite with small molecules, such as carbon dioxide. However, when this system is not in homeostasis, ONOO− can cause cytotoxicity by reacting with important biomolecules such as proteins, nucleic acids, and lipids, resulting in inhibited or altered function. For this reason, peroxynitrite has been linked to a number of disease states including cancer, stroke, myocardial infarction, atherosclerosis, hypertension, chronic heart failure, Alzheimer's disease, Parkinson's disease, multiple sclerosis, and amyotrophic lateral sclerosis. This chapter reviews the electrophoretic methods that have been developed for the separation and subsequent detection of peroxynitrite as well as its metabolites and degradation products.