Functional foods hold a great promise for future trends in human nutrition. Consumption of milk and milk products have a pronounced probiotic effects together with the expected modification of allergenic properties of milk due to the process of fermentation. The proteolytic system of lactic acid bacteria consists a cell wall bound proteinase and several intracellular peptidases, and can contribute to the liberation of bioactive peptides. Food-derived bioactive peptides are claimed to be health enhancing components which can be used for functional food. In our study we focused our attention on beta-lactoglobulin and alpha-lactalbumin in early stages of yogurt fermentation of traditional Bulgarian products. Biochemical techniques were used to measure the concentration of these two whey proteins during fermentation. At a result of the done study alteration in the concentration of beta-lactoglobulin and alpha-lactalbumin were detected. The studied proteolytic activity of the strains, used in the fermentation process confirmed the received results.