ABSTRACTProteins and amino acids were examined in cottonseed flour that had been fermented for 4 and 7 days with six selected filamentous fungi used in food processing. The fungi included Aspergillus sojae, Rhizopus oligosporus, Monascus purpureus, Actinomucor elegans, and two strains of A. oryzae. Quantities of proteins and amino acids in nonstorage, storage, and residue extracts varied among fermentations, depending on fungal species and inoculation time. Gel electrophoretic patterns of nonstorage and storage protein fractions were similar for autoclaved, but not for fermented flour; proteins in fractions from flour that was not autoclaved were distinguishable by this procedure. Protein gel patterns of fractions from the different fermentations studied showed increased numbers of small polypeptide components; quantity of protein bands in gel patterns also varied among fermentations. Isoleucine and leucine were limiting amino acids in controls and in most fermented preparations; certain protein fractions in the residue had methionine + cystine as limiting amino acids. Among fermentations, nutritional quality of storage and residual protein fractions from 4‐day treatments of the two A. oryzae strains showed the greatest improvement.