To promote application of cottonseed protein products in food industry, this work measured antioxidant activities of two water soluble protein samples (Gl-L and Gd-L) isolated in a lab scale from glandless and common glanded cottonseed meal, respectively, and one soluble protein samples (Gd-P) in a pilot scale from glanded cottonseed meal. SDS-gel electrophoresis showed that the distribution patterns of the peptide fragments in Gl-L and Gd-L were similar, but more fragments and higher molecular mass bands were observed in the Gd-P gel image. While Gd-P showed the highest activities, Gl-L and Gd-L exhibited comparable 1,1-diphenyl-2-picrylhydrazyl and hydroxyl radical-scavenging activities in most cases. In contrast, Gd-P showed lower capability of inhibition of linoleic acid autoxidation than Gl-L and Gd-L. It would be of great interest in further research on these protein fractions in food products and processes (such as roasting) involved in the protective effects of food spoilage.