Antioxidant, antimutagenic and antigenic properties of partial hydrolysates of whey and colostrum obtained using bacterial endopeptidase (alcalase) have been investigated. It was found that the depth of proteolysis, qualitative and quantitative composition of protein component of samples determined the level of their antiradical and antimutagenic activity. According to SDS-electrophoresis whey hydrolysate contains cleaved allergen proteins, whereas colostrum hydrolysate possesses a high molecular weight fraction (>10 kDa) of partially digested immunoglobulins. Proteolysis of β-lactoglobulin, which has a high allergenic potential, is confirmed by results of immunoprecipitation reaction. In accordance with the ORAC method antioxidant action of hydrolysed whey and colostrum increased by 2.8 and 5.0 times, respectively. Antimutagenic effect for whey hydrolysate was 15.7–49.2 % when tested on the strain Salmonella typhimurium TA 98 and 18.8–52.1 % for strain TA 100. It exceeded values of colostrum hydrolysate. Samples of whey and colostrum hypoallergenic hydrolysates with confirmed antioxidant and antimutagenic properties have been obtained.