The arrival of chyme in the duodenum initiate the intestinal phase and it controls the gastric activity through hormones and nervous reflexes. The duodenum firstly assist in secretion of gastric juice and then inhibit it again. The duodenum stretches masks vagal reflexes that stimulate the stomach, peptide and amino acids in the chyme that stimulate G cells to secret more gastrin. However, the acid and semi digested fats in the duodenum stimulate the enterogastricc reflex. The stomach receives inhibitory signals from the duodenum via the enteric nervous system and also medulla receives inhibitory signals from the duodenum to inhibit vagal stimulation.

A decrease in the vagal stimulation stimulates the sympathetic neurons that sends inhibitory signal to the stomach. Two hormones are involved in the duodenum namely the cholecystokinin and secretin. Cholecystokinin is found in the duodenum where it is synthesised and secreted by the enteric endocrine cells. Partially digested proteins and fats in the small intestines stimulate its production. When chyme enters the small intestine in large quantities, the cholecystokinin is released into the blood and it binds to the receptors on pancreatic acinar cells initiating a secretion of large amount of digestive enzymes.

The second hormone secretin is found in the epithelium of the small intestine produced by the endocrinocytes. Presence of acid in the duodenum cause secretion of secretin due to the flow of acid laden chyme from the stomach through the pylorus. The main function of secretin is to stimulate duct cells to secret water and bicarbonate.

The enzymes secreted by the acinar cells are flown out of the pancreas, through the pancreatic duct into the duodenum.