In Europe, two subspecies of Vipera berus, V. b. berus and V. b. nikolskii, cause most accidents of snakebites. Myonecrosis is a common local manifestation of envenomation by vipers, and both toxins with direct cytotoxicity and hydrolytic enzymes breaking down the extracellular matrix are involved in its development. Destruction of extracellular matrix results in the formation of peptides that may increase tissue damage and inflammation, contributing to endogenous intoxication, or participate in muscles regeneration. Thus, this study was aimed at analyzing the features of protein profile and proteolytic processes, as well as at evaluating the level of generation of medium and low molecular weight substances in muscle tissue after administration of V. b. berus and V. b. nikolskii venoms. We revealed a decrease in total protein content in combination with a redistribution of protein fractions towards low and very high molecular weight proteins (V. b. berus) or peptides (V. b. nikolskii), an increase in total proteolytic activity, changes in the profile of gelatinolytic enzymes and a rise in the generation of medium and low molecular weight substances, all of which may indicate the intensification of proteolysis in rat muscles after injection of the studied venoms. Significant differences in the effects of studied venoms were also established.