Serologic screening of a rabbit breeding colony over a 9-month period showed that all 9-week-old rabbits with Encephalitozoon cuniculi infection were born of E cuniculi-infected does. This observation, obtained from studies on 395 young rabbits, suggested that transmission of infection is either transplacental or the result of close contact soon after birth. On this basis, 16 young healthy rabbits, seronegative to E cuniculi, were isolated and tested at 2-week intervals for antibodies to E cuniculi. In the first 2 months, seven rabbits showed indications of developing antibodies to E cuniculi and were immediately removed from the colony. The remaining rabbits along with their 52 offspring were tested for serum antibodies for a further 16 months and no rabbit became seropositive. Eight months after establishment of the colony, three does, one buck and six 12-week-old rabbits were killed. Macroscopic and extensive histologic and immunofluorescence examinations failed to reveal any evidence of infection with E cuniculi. These results showed that serological screening for E cuniculi infection by immunofluorescence is a simple yet adequate procedure for establishing a rabbit colony free of encephalitozoonosis.