Oxidative stress is present in cardiovascular diseases and hyperhomocysteinemia, an independant risk factor for these diseases. It may play a role by inducing production of oxygen free radicals. Reduced glutathione is the most abundant intracellular low-molecular-weight thiol and plays an essential role in protecting cells from toxic species. The thiol-containing compounds which are the most often considered in biological analysis, are homocysteine (Hcy), cysteine (Cys), glutathione (GSH), cysteinyl-glycine (Cys-Gly), gamma-glutamyl-cysteine (gammaGlu-Cys), and their derivatives. These aminothiols are present in body fluids or cells, associated with proteins or occur free (reduced and oxidized). These free forms may play a role in the pathogenesis of disease. Because Hcy (with Cys) exhibits pro-oxidative properties and GSH (with Cys-Gly) antioxidative properties, and because there is extensive interconversion between these metabolites, their simultaneous analysis in biological samples is necessary to examine their role in human disease. Capillary electrophoresis (CE) seems to be a solution to reach this goal. No extensive review reports the analysis of aminothiols using CE. This review describes the different CE approaches which have been used to separate and assay aminothiols, and the different obtained datas.