The aim of this study was to investigate the prevalence of Encephalitozoon cuniculi antibodies in healthy and diseased rabbits in Germany. Age and gender dependencies were taken into consideration. The sensitivity of the E cuniculi antibody test and its relevance for the diagnosis of E cuniculi infection in rabbits was also examined. A total of 773 healthy and diseased rabbits were tested for E cuniculi antibodies (indirect immune fluorescence antibody test (IFAT) or carbon immunoassay (CIA). No differences between diseased and healthy rabbits were observed with regard to gender, but diseased rabbits were significantly older (P>0.001). Forty-three percent (336/773) of all rabbits were positive for E cuniculi antibodies. Of the diseased rabbits, 48 per cent (266/555) were positive for E cuniculi antibodies. While 96 per cent (91/95) of the rabbits with histopathologically or PCR confirmed encephalitozoonosis were E cuniculi antibody-positive, only 60 per cent (144/241) of the rabbits suspected of E cuniculi infection were antibody-positive. Of the healthy rabbits, 18 per cent (39/218) were positive for E cuniculi antibodies. Diseased rabbits were almost three times more likely to be E cuniculi antibody-positive than healthy ones (P>0.001; relative risk (RR): 2.68; 95% CI 1.99 to 3.61). The sensitivity of the E cuniculi antibody test was 96 per cent.