A complex study of the protein composition of the biologically active components of the extracts of the velvet deer antlers (VDA, include Cervus nippon and Cervus elaphus) using two-dimensional gel electrophoresis (2D-PAGE), size-exclusion chromatography (SEC), and peptide mapping with high-performance liquid chromatography with mass spectrometric detection (HPLC-MS) with the use of fermentation by trypsin was done. A molecular-mass distribution characteristic for protein extracts of VDA has been established. Optimal conditions for extraction, chromatographic separation and relative quantitative determination of the main components have been determined. The results of the identification of the most significant (major and minor) protein components in the extracts of the studied objects are described in detail in accordance with the algorithm of the search program Spectrum Mill MS Proteomics Workbench and the protein database Uniprot. The data of protein profiling are clustered according to molecular and biological functions. The connections of the identified proteins with possible mechanisms of biological action and targets, which can be affected by the protein components of the studied objects, are presented. Based on the results of the study, conclusions about the multicomponent protein composition of extracts of VDA were drawn. The marker protein components in the studied extracts are suggested and the possible interrelationships of the detected proteins in the extracts with biological effects are indicated.