A group of authors has developed a multilevel mathematical model that focuses on functional disorders in a human body associated with various chemical, physical, social, and other factors. At this point, the researchers have come up with structure, basic definitions and concepts of a mathematical model at the "macrolevel" that allow describing processes in a human body as a whole. Currently we are working at the "mesolevel" of organs and systems. Due to complexity of the tasks, this paper deals with only one meso-fragment of a digestive system model. It describes some aspects related to modeling multiphase flow in the antroduodenal portion of the gastrointestinal tract. Biochemical reactions, dissolution of food particles, and motor, secretory, and absorbing functions of the tract are taken into consideration. The paper outlines some results concerning influence of secretory function disorders on food dissolution rate and tract contents acidity. The effect which food density has on inflow of food masses from a stomach to a bowel is analyzed. We assume that the future development of the model will include digestive enzymes and related reactions of lipolysis, proteolysis, and carbohydrates breakdown.