Microsporidia are typically parasites of invertebrates (Canning EU, J Lom. 1986. The Microsporidia of Vertebrates. Academic Press, New York, 289 pp.). They are characterized by having spores that contain a tubular filament through which the nuclear material is extruded directly into the host cell that is being infected. There have been only four reports of microsporidia infecting domestic cats.

The predominant microsporidian parasite of mammals is Encephalitozoon cuniculi which is considered mainly a parasite of rabbits and small rodents. The spores are passed in the urine and hosts become infected by the ingestion of the spores. Once ingested, host cells are penetrated, and the organisms are found in the vascular endothelium throughout the body. The major organs affected are the kidney and brain, although organisms can be found in almost any tissue. Carnivores can apparently become infected by the ingestion of infected rodent or lagomorph hosts that contain hundreds to thousands of spores. As noted for dogs and foxes, if hosts become infected while pregnant, there can be transuterine infection with pronounced deleterious effects on the offspring.