In this study, the humoral mucosal immune response to a recombinant Eimeria antigen (Ea1A) was enhanced using cholera toxin (CT). Chickens were primed intra-intestinally with Ea1A either conjugated or not to CT. The local and systemic antibody responses to both Ea1A and CT were determined to find out whether the chickens could respond to CT and whether both antigens had reached the lamina propria. In addition the effects of CT on lamina propria leukocytes were examined. The results showed that chickens had receptors on the caecal epithelium that could bind CT. At day 7 after administration, the number of CD4 and CD8 T lymphocytes in the lamina propria of the caecum had increased, indicating that CT had a specific immunological effect. At this timepoint, anti-CT antibody containing cells were detected locally in the lamina propria of the caecum. In serum all antigen preparations containing CT induced IgM and IgG antibody titres specific for CT within 10 days after priming. In addition, the recombinant Ea1A antigen also induced serum responses when administered together with CT or conjugated to CT, thus both CT and the antigen had reached the lamina propria. Nevertheless, the Ea1A specific response was much higher in the primary response and after booster immunization when the antigen was conjugated to CT than when only mixed with CT. Therefore, we conclude that CT is a suitable adjuvant for intra-intestinal application in chickens, especially when the antigen is conjugated to it.