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Parasites and other infections have many effects on the gastrointestinal tract of individuals who are immunocompromised. Few reviews focus on parasitic infections, which are covered here.The review first examines recent advances in our understanding of the taxonomy, diagnosis and treatment of pathogens such as cryptosporidia, cyclospora, isospora and microsporidia, which are recognized causes of diarrhoea in the immunocompromised, and discusses possible links between amoebiasis and HIV. The complex interactions of both intact and abnormal immune systems with helminth infections such as hookworm and strongyloidiasis, and with trematode infections such as schistosomiasis, are receiving increasing attention. These are discussed, together with the novel concept of using live helminths to treat inflammatory bowel disease.Parasitic infections remain a significant problem for immunocompromised individuals in resource-poor settings, and further work is needed to develop accessible diagnostic tests and to improve our understanding and management of their pathogenic effects. New concepts about the interactions of helminths with host immunity suggest the need for collection of further epidemiological and clinical data to unravel the complexities of such immunological interactions.