Peptides are among the important biologically active substances. In recent decades, great efforts have been made by scientists to develop and produce short (low molecular weight) peptides that exhibit higher pharmacological properties than their prototypes. The source of natural peptides with high biological activity can serve as secondary fish raw materials – waste obtained during fish cutting. A large amount of fish collagen-containing waste accumulates at the fish processing enterprises of the Kaliningrad region. The article describes the possibility of obtaining low-molecular-weight peptides from secondary collagen-containing fish raw materials by combined hydrolysis methods combining both enzymatic and thermal treatment. Secondary fish raw materials have been studied and used- sardine scales, walleye heads, river perch ridges and salmon skin. The processes of protein splitting of raw materials under the action of three types of hydrolysis in an aqueous medium – enzymatic-thermal, thermal-enzymatic and thermal-enzymatic-thermal have been studied. In the experiments, the enzyme preparation of microbiological synthesis Alcalase® 2,4 L from Novozymes, Denmark, and an experimental enzyme preparation from the digestive organs of bream, manufactured on the basis of Biotech LLC, have been used. It has been revealed that the combined two- and three-stage hydrolysis methods provide the maximum yield of protein hydrolysates with low molecular weight peptides. The molecular weights of peptides, amino acid composition have been studied and a high biological value of the obtained protein hydrolysates with low molecular weight peptides has been established. The presence of all essential amino acids in hydrolysates has been determined, as well as an increased content of proline, glycine, alanine, glutamic and aspartic acids, which are necessary to increase immunity, ergodynamics of the body and the work of the human musculoskeletal system.