In this study trypsin (TIA) and chymotrypsin inhibitory (CIA) activities were determined in the extracts of wheat, rye mix, mixed cereals and, whole wheat flours and, breads made with these flours. In addition, effects of fermentation, baking and in vitro digestion on TIA and CIA were studied. Whole wheat flour, dough, and bread did not show any TIA. Other flours displayed TIA. Contrary to, all flours, doughs, and breads exhibited CIA. Although TIA was not detected in the protein extracts obtained from wheat and rye mix breads, protein extract of rye mix flour exhibited TIA. Following in vitro digestion process, TIA of wheat bread was found as 5.91units/mL gastric dialysate and 9.17units/mL intestine dialysate. CIA was determined in dialysates obtained from wheat (2.12CI/mL and 3.78CI/mL for gastric and intestinal dialysate respectively) and rye breads (4.16CI/mL and 2.46CI/mL for gastric and intestinal dialysate respectively).