Technical Abstract: An improved method for separating and characterizing maize and sorghum storage proteins by free zone capillary electrophoresis (FZCE) was developed by mimicking reversed-phase high-performance liquid chromatography (RP-HPLC) conditions. This FZCE buffer system consisted of 80 mM phosphate-glycine buffer, nominal pH 2.5, containing 60% ACN and hydroxypropylmethyl-cellulose. Resolution was similar to or higher than that previously achieved by FZCE buffers utilizing 8M urea as a buffer additive. ACN concentrations of at least 50% were necessary to achieve acceptable separations; this ACN concentration is approximately that necessary to extract these storage proteins. ACN was equally effective as traditional ethanol solvents and 8M urea for solubilizing maize and sorghum proteins. The ACN based FZCE buffer system gave high repeatability (<0.3% relative standard deviation, measured over 15 consecutive injections) for migration time. Subclasses of maize and sorghum storage proteins were identified, and genotypes of each cereal were successfully differentiated using ACN containing buffers. This FZCE method may be applicable for the analysis of other hydrophobic proteins without the use of urea.