Oligomeric procyanidins are potent antioxidant polyphenols of potential interest as disease-preventing agents. Their efficiency depends on the size and composition of their oligomeric structures. The mean degree of polymerization of these compounds is usually estimated by thiolysis. with thiol-alpha-toluene followed by analysis using high-performance liquid chromatography (HPLC). We show the development of a mixed micellar electrokinetic chromatography (MEKC) method for the separation of the major components obtained after thiolysis with cysteamine (catechins and their cysteamine conjugates). MEKC studies using sodium dodecyl sulfate (SDS as pseudostationary phase led to long migration times, e.g., with 100 mM SDS, at pH 7, the solutes were separated in about 40 min), while the use of sodium cholate (SC) produced an elution window relatively short. Using a mixed micellar SC-SDS system (50 mM phosphate at pH 7 containing 40 mM SC and 10 mM SDS), it is possible to separate these compounds in less than 15 min. The proposed method is useful to separate the major components of the thiolysate in effluents from food processing (e.g., skins and seeds from grape and apple) considered as potential procyanidin sources.