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, as well as effector cells and molecules, all of which are 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. This book presents and discusses current research in the study of mucosal intestinal immunity and response to parasite infections in ectothermic vertebrates.