The digestibility of sorghum protein is reduced when wet cooked. Size exclusion chromatography (SEC) together with other protein analytical techniques was applied to further elucidate the effects of cooking on the sorghum and maize and their prolamin proteins. Sorghum and maize meal and their respective tertiary butanol extracted kafirin and zein were wet heat treated by boiling or pressure cooking. As expected, the in vitro pepsin protein digestibility of sorghum meal and kafirin reduced with boiling and pressure cooking, whereas the decrease in maize meal and zein protein digestibility was much less. SDS-PAGE showed that the boiled and pressure-cooked kafirin was more polymerized than the corresponding zein preparations. SEC of kafirin also revealed a substantially increased high molecular weight peak with boiling and pressure cooking. In contrast, the high molecular weight peak was very small for control and wet heated treated zein. The highly polymerized kafirin occurs as a result of extensive disulfide bonding of kafirin monomers during cooking. Cooking sorghum meal and kafirin also resulted in a relative change in secondary structure from alpha-helical to beta-sheet, as determined by Fourier transform infrared spectroscopy. The pepsin indigestible kafirin residues were mainly in beta-sheet conformation. In contrast, the conformational changes were very small for cooked maize meal and zein. Disulfide bonds formed during heating cause polymeric kafirin formation and also promote realignment of kafirin into beta-sheet structures. These conformational changes apparently cause the lower proteolysis susceptibility of kafirin.