Serum samples from 237 randomized rabbits from the five ecological zones of Nigeria, i.e. Northwest (NW), Northeast (NE), Southeast (SE), Southwest (SW) and Northcentral (NC), were evaluated for the presence of antibodies to Encephalitozoon cuniculi by the indirect immunofluorescent antibodies test. A titre of 10 or more was taken as positive. Thirty-nine (16.5 %) of the 237 samples were positive with 11, 10, 8, 6 and 4 seropositive rabbits occurring in the NW, NE, SE, SW and NC zones of Nigeria, respectively. Age, sex, live mass and access to grass as a feed supplement were not statistically (P > 0.05) associated with seropositivity, but cage type (single-versus multi-rabbit type), contact with free-range rats and previous illness were strongly (P < 0.05) associated with it. The practice of selling unscreened and untreated 5 to 10-week-old weaners to prospective buyers as foundation stock, use of multi-rabbit communal cages, occasional release of rabbits in runs and contact with free-range house rats should be discouraged. Regular prophylactic and curative treatments, occasional serological screening to remove carriers, and the practice of a high level of hygiene in rabbit colonies are effective control measures.