The effect of hydrolyzed casein (HC) on the expression of three mucin genes (Muc2, Muc3, and Muc4) in the rat intestine was investigated using quantitative real-time polymerase chain reaction. After a 10 day acclimatization period, rats received for 8 days the test diets containing either HC or a synthetic amino acid (SAA) mixture as the sole source of nitrogen or a protein-free (PF) diet (n = 12 per treatment). The addition of HC or the SAA mixture to the diet significantly improved average daily gain, average daily food intake, and gain:feed ratio as compared with the PF diet. Terminal ileal endogenous N flow was significantly higher for the HC-fed rats in comparison with either the SAA or the PF rats (p < or = 0.001). HC supported a significant increase of Muc3 mRNA (277 and 229% of that for diets PF and SAA, respectively; p < or = 0.05) in the small intestinal tissue and Muc4 mRNA (325 and 265% of that for diets PF and SAA, respectively; p < or = 0.05) in the colon. In conclusion, HC enhances ileal endogenous N flow and up-regulates in vivo the expression of some individual mucin genes.