This paper explores the ability of Lactobacillus helveticus strains to release sequences of short biologically active peptides (containing 2–10 amino acid residues) from casein. The proteolytic enzymes of the tested strains exhibit different patterns of cleavage of CN fractions. The modification of κ-casein (κ-CN) with pyrrolidone carboxylic acid inhibits the proteolytic activity of strains L. helveticus 141 and the reference strain (DSMZ 20075), while the modification with phosphothreonine inhibits enzymes of all the tested bacteria. The peptide sequencing analysis indicated that the examined strains produced functional peptides very efficiently. κ-CN proved to be the main source of short peptides released by bacterial enzymes, and the hydrolysis of κ-CN yielded eighty-two bioactive peptides. The hydrolysis of αS2-casein, αS1-casein, and β-casein yielded six, two, and one short-chain bioactive peptides, respectively. The isolated bioactive peptides exhibited antioxidative, opioid, stimulating, hypotensive, immunomodulating, antibacterial, and antithrombotic activities. A vast majority of the isolated bioactive peptides caused inhibition of the angiotensin-converting enzyme and dipeptidyl peptidase IV. The role of hydrolysis products as neuropeptides is also pointed out. The highest number of cleavage sites in κ-casein and functional activities of short-chain peptides were obtained in hydrolyzates produced by L. helveticus strain T105.