This study is a contribution on the knowledge on the nature of color problems associated with cottonseed kernel flours in some technological treatments. The influence of total gossypol, shell and moisture content on the color of experimental flours were measured in terms of Hunter L, a, b parameters. Total gossypol, shell and moisture content were positively correlated to the difference of color (Delta E). The discolouration of flours by extracting colouring compounds with hydroalcoholic solvents has shown that this action is difficult to be achieved. Intrinsic colouring compounds of flours identified by thin layer chromatography were found to be gossypol and derivatives, flavonoids and phenolic acids.