As part of the mucosal immune system, the intestine plays a paramount role in the immune response in all vertebrates. The mucosal immunity includes inductive and effector tissues, and effector cells and molecules, all part of both innate and adaptive immunity and their connections. The digestive tract is the target organ of many parasites. In ectotherms, intestinal parasites include mainly flagellates, apicomplexans, myxozoans and helminths. The gut mucosal epithelium acts as a protective barrier against pathogens. Intestinal mucins and terminal carbohydrate residues are involved in the first contact pathogen-host, in some occasions through interaction with parasite lectins, as illustrated by mammalian and reptile Entamoeba spp. Mucins and their glycosylation patterns can change in reponse to intestinal parasites, including several piscine myxozoans and helminths. In addition, different pathogen recognizing receptors (PRRs) are sensed by the pathogen-associated molecular patterns (PAMPs) of invading pathogens. Although several PRRs have been thus far identified in ectotherms, little or no information is available on their presence in the intestine or on their involvement in parasite recognition. However, in mammals, several PRRs, mainly Toll-like receptors (TLRs) and nucleotide-binding oligomerization domains (NODs) play a significant role at the intestinal level by sensing pathogens and controlling inflammation and apoptosis, thus contributing to the maintenance of homeostasis. Several molecules and factors related to acute phase response (APR), such as AMPs, lysozyme, lectins, complement, cytokines and antiproteases can be activated at the gut level, in connection with innate and adaptive immune factors. Cellular components are also crucial in the intestinal immune response, and they include intestinal epithelial leucocytes (IECs), dendritic cells, macrophages, granulocytes and intraepithelial lymphocytes (IELs), all of them interacting at both the mucosal and systemic levels, to orchestrate an integrated immune response. The cross-talk between the different cellular types, involving also TLRs, AMPs, cytokines and other factors is well known in endotherms. The cellular reactions to several mammalian intestinal parasites are also well characterized. However, information is much scarcer for ectotherms. Although several types of immune cells (EGC/mast cells, other ganulocytes, rodlet cells (RCs), T and B cells, neuroendocrine cells) have been identified (mainly in teleosts), these cells are not well characterized and the knowledge of the different T cells subsets is in its infancy. In addition, though inflammatory reactions to several intestinal studied parasites have been reported, the cellular responses have been characterized for few species, mainly Enteromyxum spp. Available information points to the relevant role of RCs and EGCs/mast cells, but the cellular types have not been fully characterized, and the involvement of other granulocytes remains to be elucidated. In addition, the T and B cell responses and the role of secretory immunoglobulins are poorly known.