Protein inhibitors of peptidases are widely distributed among animals, plants, and microorganisms. They are important regulatory molecules that function to avoid proteolysis in various biological systems. From the plasma of animals that are naturally resistant to snake envenomation, a special class of peptidase inhibitors has been identified. These inhibitors have antihemorrhagic properties and form inactive noncovalent complexes with snake venom metallopeptidases. In nonresistant animals, these toxic metallopeptidases induce microvascular damage and are responsible for systemic and local hemorrhage, key events in the pathogenesis of viperid envenomation. The inhibitors isolated from mammalian plasma are grouped into the MEROPS I43 family of immunoglobulin-related proteins; those from reptiles show a typical cystatin-like fold and belong to the MEROPS I25C subfamily. The inhibitors show a reversible tight-binding reaction mechanism of inhibition, although due to a lack of three-dimensional information for the enzyme-inhibitor complexes, the structural features that govern the interaction are largely unknown. This review is intended to highlight the latest advances in the field, analyzing future perspectives in the area of natural immunity against snake venom. The discussion will focus on how endogenous protein inhibitors can be used as structural templates, providing valuable insights into the molecular determinants of selective metallopeptidase inhibition. The wide range of natural toxin inhibitors may constitute a rich source of information leading to new possibilities in intervention not only against snake venom metallopeptidases but also against other metzincins, such as mammalian MMPs and ADAMs.