The exquisite sensitivity and selectivity of contemporary protein analysis means that proteomics is increasingly at the forefront of biomedical investigation. The molecular basis of diseases states can now be revealed at the protein level, complementing transcript and genomics data. Moreover, protein biomarkers are increasingly accessible to the scrutiny of the protein chemist. The focus of these studies has been on human systems but diseases that occur naturally in nonhuman mammalian species may provide additional perspectives on the pathophysiology of human disorders. As a result, veterinary research aimed at promoting animal health may lead to concomitant improvements in the characterisation, clinical management and treatment of human diseases. This review will focus on the use of proteomic approaches to study naturally occurring disease states in animals and discuss ways by which these investigations may advance the health of both animals and humans.