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Background: Encephalitozoon cuniculi is a microsporidian parasite commonly found in rabbits that can infect humans, causing encephalitozoonosis. Our objective in this study was to evaluate the seroprevalence of this parasite in rabbits and humans in China Methods: Overall, 300 serum samples each from clinically healthy rabbit and human were collected from three regions of China (Sichuan Province, Chongqing Municipality and Jilin Province) from January to September 2013 and tested for anti- E. Cuniculi antibodies using an ELISA. Results: An overall seroprevalence of E. cuniculi was recorded as 56/300 (18.76%) and 29/300 (9.76%) in rabbit and human sera, respectively. The seropositivity of rabbit samples collected from Jilin province was 41%, which was significantly higher (P<0.01) than Sichuan Province (9%) and Chongqing Municipality (6%). Three breeds of rabbit were used in the present study and antibody detection in Rex Rabbit was significantly (P<0.01) higher than Japanese White and New Zealand Rabbit. In human, Jilin province was more prevalent (18%) followed by Sichuan Province (6%) and Chongqing Municipality (5%). Conclusions The E. cuniculi was present and widespread among healthy rabbits and humans in China [ABSTRACT FROM AUTHOR]