Zein isolation by aqueous ethanol extraction from dry-milled corn produces a mixture of zeins, covalently linked polymers (dimers, tetramers, etc.) and higher-molecular-weight aggregates, some of which were not soluble in aqueous alcohol. The insoluble particles were identified as protein aggregates which form when the extraction solution is heated, particularly under alkaline conditions. The insoluble protein aggregates were not present in zein isolated by the same method from corn gluten meal. Zeins extracted from corn gluten meal and dry-milled corn were fractionated (by differential solubility) to identify differences in their polypeptide compositions. Using polyacrylamide gel electrophoresis, beta- and gamma-zeins were detected in dry-milled corn, but only trace amounts of beta-zein were found in corn gluten meal. Treatment of dry-milled corn with 0.55% lactic acid and 0.2% sulfur dioxide at 50 degrees C for 6 h before ethanol extraction resulted in a 50% increase in zein isolate yield with high solubility (98%). This pre-extraction treatment cleaved disulfide linkages of the beta- and gamma-zeins and significantly reduced insoluble aggregates in zein isolates.