Transesterification of cottonseed oil was carried out using ethanol and potassium hydroxide. A central composite design with six center and six axial points was used to study the effect of catalyst concentration (0.5 to 1.5 % wt/wt), molar ratio of ethanol to cottonseed oil (3:1 to 20:1) and reaction temperature (25 to 75 °C) for percentage yield and percentage initial absorbance (%A385nm) of the biodiesel. Maximum predicted percentage yield of 98 % was obtained at a catalyst concentration of 1.07 % (wt/wt) and ethanol to cottonseed oil molar ratio of 20:1 at reaction temperature of 25°C. Optimal yield in the range of 95–98 % were obtained along a ridge extending over the entire range of molar ratios studied and over a range of 1.07-1.5 % (wt/wt) for catalyst concentration. Along this high-yielding ridge, very low %A385nm were obtained with a maximum of 24 % at a catalyst concentration of 1.5 % (wt/wt) and ethanol to cottonseed oil molar ratio of 3:1. Maximum predicted %A385nm of more than 85% was obtained at 0.5 % (wt/wt) catalyst concentration and molar ratio of 3:1 at 25°C. The response surfaces describing % yield and %A385nm were inverse with the antioxidant, gossypol, contributing to the absorption. Gossypol is currently under investigation as an antioxidant in biodiesel fuels as well as a potential anticancer compound. The glycerol fraction also contains the remaining fraction of gossypol that may be purified for further exploitation.