Encephalitozoon cuniculi is an intracellular protozoon parasite of brain, kidneys and other tissues. It frequently causes chronic and latent infections in laboratory animals especially rabbits (Shaduck and Pakes, 1971). Numerous serological tests have been developed for the diagnosis of encephalitozoon's. These included the in- direct fluorescent antibody tests (IFAT) (Chalupsky, et al. 1971); carbon immunoassay (CIA) (Waller, 1977 and Kellett & Bywater, 1978); immunoperoxidase test (IPT) (Gannon, 1978); skin hypersensitivity test (SHT) (Pakes, et al., 1972); complement fixation test (CFT) (Wosu, 1975) and haemoagglutination test (HAT) (Hubner, et al. 1973). Toxoplasmosis is a widespread disease of mammals, bird, man and laboratory animals including rats, mice, guinea pig, rabbits, dogs and cats. The most common serological test used for diagnosis of toxoplasmosis are sabin feldman dye test, indirect fluorescent antibody test, enzyme linked immunosorbent assay, indirect hemagglutination test and carbon immunoassay (Waller and Bergquist, 1982; Dubey and Beattie, 1988). Carbon immunoassay is a rapid, easy and reliable serological test as compared with other tests for diagnosis of encephalitozoonosis and toxoplasmosis in rabbits (Waller 1977; Waller and Bergquist, 1982). Hence, the present study aims to study the seroprevalence of E. cuniculi and T.gondii in rabbits by CIA since the information on this subject in Egypt are lacking.