Encephalitozoon cuniculi is an obligatory intracellular microsporidian parasite that can infect a wide range of mammals, including rodents, rabbits, horses, carnivores and humans, in which the organism is known as an opportunistic pathogen of immunocompromised individuals. Nevertheless, the main host for E. cuniculi is the rabbit and infections usually have a sub-clinical course. However, severe disease is recognised in pet rabbits more frequently within the last years. As the central nervous system, the kidney and the eye are predilection organs for the organism, predominant histopathological alterations comprise granulomatous meningoencephalitis, chronic interstitial nephritis and phacoclastic uveitis. A definitive diagnosis of encephalitozoonosis in vivo is difficult, but it is important for specific treatment and the determination of possible zoonotic risks. This review article covers epidemiology, pathology, pathophysiology, immunology, clinical signs, differential diagnosis, diagnosis and treatment of encephalitozoonosis in rabbits.