The effect of treating nonlinted whole Pima cottonseeds (WCS) with heat, NaOH, or their combination on digestive tract digestibility in dairy cows, was studied using the mobile dacron bag technique. NaOH treatment increased ruminal DM disappearance from WCS. For DM there was an interaction, between heat treatment and incubation time. Interactions of NaOH x heat and heat x incubation time were found for ruminal CP disappearance. Heat treatment decreased ruminal CP disappearance. With WCS which was heat-treated in the presence of NaOH, ruminal CP disappearance decreased. NaOH and heat treatments of WCS, respectively, increased and decreased intestinal DM disappearance. These respective treatments also increased and decreased intestinal CP disappearance. NaOH and heat treatments of WCS, respectively, increased and decreased total tract DM and CP disappearance. It was concluded that a combination of NaOH and heat treatments may protect nonlinted WCS from excessive ruminal CP degradation and deliver more nutrients to the intestine.