This paper describes a presumptive case of encephalitozoonosis in a rabbit (Oryctolagus cuniculus), examining two common presentations of this disease. Encephalitozoon cuniculi is an obligate intracellular microsporidian whose chief host is the rabbit. Although seroprevalence is high, many infections are subclinical. Affected animals may develop neurological, renal, or ocular manifestations of E. cuniculi. The difficulty in diagnosis and management of this disease is emphasized. The nature of the microsporidia as well as their life cycle and recent changes in classification of this agent are also highlighted. Encephalitozoonosis is an increasingly common problem in pet rabbits, and furthermore, with the emergence of AIDS in 1980s, E. cuniculi and other microsporidia have become a zoonotic concern for the immunocompromised human population.