Twenty‐one Lactobacillus strains isolated from three types of Balkan homemade yogurts were grown on sodium caseinate, β‐casein or whey proteins, and the proteolysis was followed by electrophoresis and reversed‐phase high‐performance liquid chromatography. The best conditions allowing obtaining proteolysis without casein precipitation are 0.8% casein in 50‐mM phosphate buffer. The strains tested showed a relatively high proteolytic activity despite the limited conditions for bacterial growth. Within 72 and 96 h of incubation, 80–90% of β‐casein was consumed. They showed also a proteolytic activity toward α‐lactalbumin (ALA), being able to reduce its concentration between 5 and 55%, depending on the strains used. The capacity of the strains to hydrolyze β‐lactoglobulin was lower as compared with hydrolysis of ALA. Hydrolysis of casein by all strains produced peptides with an antibacterial effect against Escherichia coli. Consequently, to obtain a maximal hydrolysis of the dairy proteins seconded by appearance of antimicrobial peptides, a combination of strains with different beneficial properties to be used as starters was proposed. PRACTICAL APPLICATIONS Some of the 21 Lactobacillus strains isolated from three types of Balkan homemade yogurts may be used to proteolyze milk proteins in order to produce peptides with an antibacterial effect against Escherichia coli. To obtain a maximal hydrolysis of the dairy proteins seconded by appearance of antimicrobial peptides, a combination of strains with different beneficial properties to be used as starters should be determined. During fermentation process, milk proteins are acidified by the production of lactic acid and are hydrolyzed by proteases and peptidases from bacteria. This proteolysis is followed by a reduction of the number of epitopes and consequently by a decrease in allergenicity of hydrolyzed proteins. For these reasons, starters as Lactobacillus strains with beneficial properties able to reduce the allergenicity of fermented milk products are of great interest for the dairy industry.