Three different varieties of cottonseed (S1, S2, and S3) were dehulled, separated, and defatted by hexane extraction under controlled conditions (moisture < 3%, temperature < 50 degrees C). The defatted flours, designated as CS1 and CS2 (glandless) and CS3 (glanded), which had free-gossypol levels of 0.15, 0.28, and 0.68%, respectively, and protein levels of 61.4, 61.7, and 58.5%, respectively, were taken for aqueous extraction using NaOH as the alkali in the presence of Na2S2O4, a reducing agent. The extract, after centrifugation, was immediately taken for ultrafiltration (UF) using polysulfone membranes, followed by diafiltration(DF). Experiments at 40 and 60 degrees C, to examine the UF performance and gossypol binding effect, were carried out with strict control of the feed pH. The intensely yellow-colored permeates, probably due to alkali-soluble sodium gossypolate and gossypol-like pigments, were checked for color intensity as a qualitative measure in ultrafiltration concentrate. The intensity was found to be on the decline, less during UF and more during diafiltration. The final UF/DF dried products were analyzed for free gossypol (FG), bound gossypol (BG), total gossypol (TG), and protein. Protein isolates (PI) from Samples CS1 and CS2 were found to have very low FG, with little effect of the processing conditions on binding of gossypol with the protein. PI from Sample CS3 was found to have slightly high FG with relatively high BG. The effect of temperature was found to result in high permeation rates without much effect on the rejection of the components and the binding of gossypol. The gossypol and protein contents of three UF/DF dried proteins were 0.006, 0.012, and 0.041% FG, and 89.4, 90.1, and 86.4% protein. The colors of PI from Samples CSI and CS2 were lighter while PI from Sample CS3 was relatively darker.