The proteins of wheat flour have several biological activities that can affect human health and physiology when wheat-based foods are consumed. The modifications of bread crumb and crust proteins during an in vitro peptic/pancreatic digestion process were studied by electrophoresis and immunoblotting with polyclonal antibodies specific for single proteins or groups of homologous proteins of the wheat flour, and the results were compared to those obtained for an unheated dough sample. The results show that baking affects the extent of proteolysis and the immunological and physicochemical features of the digestion products in relation to the level of the heat treatment. Therefore, the results concerning the digestion of the unheated wheat flour or dough are not representative of what happens when baked products enter the human digestive tract.