Inborn errors of metabolism are caused by genetic defects in intermediary metabolic pathways. Although long considered to be the domain of human paediatric medicine, they are also recognised with increasing frequency in companion animals. The diagnosis of diseased animals can be achieved by searching for abnormal metabolites in body fluids, although such screening programmes have, until now, not been widely available to the small animal clinician. A comprehensive battery of analytical tools exists for screening for inborn metabolic diseases in humans which can be applied to animals and serve not only for the diagnosis of affected patients but also to detect asymptomatic carriers and further our understanding of metabolic pathways in dogs and cats. Moreover, naturally occurring animal models of inherited metabolic diseases provide a unique opportunity to study the biochemical and molecular pathogenesis of these disorders and to investigate possible therapeutic options.