Diseases that are associated with infections or allergic reactions in the gastrointestinal and respiratory tracts are major causes of morbidity in both cats and dogs. Future strategies for the control of these conditions require a greater understanding of the cellular and molecular mechanisms involved in the induction and regulation of responses at the mucosal surfaces. Historically, the majority of the fundamental studies have been carried out in rodents or with tissues obtained from man, but the expanding range of reagents available for the study of farm and companion animals provides opportunities for study in a wider range of animals including cats and dogs. To date, these studies have tended to be focussed on characterising the cellular distributions in healthy animals and in groups of cats and dogs identified as having an increased risk of mucosal disturbance. Where species comparisons of mucosal immune systems have been made, the results have tended to be divided between monogastric and ruminant animals. It is then not surprising that the mucosal immune systems of both cats and dogs bear greatest similarity to that documented for man and pigs. For example, IgA is the dominant immunoglobulin in mucosal secretions of cats and dogs and oral tolerance can be induced following the introduction of novel antigens into the diet. Also like several other species, cats become transiently hypersensitive to the newly introduced dietary antigen prior to the establishment of tolerance. In contrast, there are a number of potentially important differences. In particular, there are significant differences between cats and dogs in the expression MHC class II molecules on gut epithelial cells. Similarly, it has been reported that cats have elevated numbers of intraepithelial lymphocytes (IEL) and that a proportion of these express surface IgM. It remains to be determined if these differences reflect the way in which the animals are maintained and if they may have greater biological significance.