The circadian variation in protein content in the digestive tract was studied in parallel with food intake in the free-feeding rat maintained under a 12:12 hr light:dark cycle (lights on at 07 hr). Rate of ingestion of a casein-based diet increased progressively during daytime, but most of the intake occurred in the dark. Gastric emptying of proteins lagged by a 3-hr interval behind intake. N content in the intestine divided equally into three segments also increased in the dark. The rise was specific for each segment with the most marked rise in the second segment. Endogenous N levels were high and accounted for at least two thirds of intestinal N levels. There was no net absorption of N in the first intestinal segment due to dilution by endogenous proteins. Absorption was at an average of 70% in the second segment and reached 85% in the distal intestine. The amino acid composition of intestinal protein content reflected endogenous proteins much more than casein. Specific trypsin activity increased distally. The appearance of nitrogenous material (alpha-amino N) in portal blood also followed a circadian variation reflecting the pattern of food intake. In spite of their high level in the intestine, endogenous proteins did not lead to an appreciable appearance of nitrogenous material in the blood except at 10 hours. Results indicate that fluctuation in food intake is accompanied by complex variations in protein contents of the digestive tract. Endogenous protein levels were high and seemed to have a slow turnover.