Eimeria intestinalis is the most pathogenic species of rabbit coccidiosis, causing weight loss, diarrhea, and even acute death. The currently used anticoccidial drugs against E. intestinalis in rabbits are associated with drug resistance and residues. Immunological control might be a potential alternative. We cloned and expressed the E. intestinalis recombinant EF1 alpha and EFG (rEi-EF1 alpha and rEi-EFG, respectively). Rabbits were immunized subcutaneously every 14 days with 100 mu g of rEi-EF1 alpha and rEi-EFG and followed by 5 x 10(4) E. intestinalis sporulated oocysts orally challenge. Serum samples were collected every 7 days to measure the levels of specific antibodies and cytokines. On post-challenge day 14, rabbits were sacrificed and the anticoccidial index was evaluated. The rabbits of PBS challenged groups exhibited anorexia, diarrhea, marked intestinal wall thickening, and white nodules that formed patches, while rabbits from the rEi-EF1 alpha or rEi-EFG challenged group exhibited milder symptoms. The rEi-EF1 alpha group showed a 75.18% oocyst reduction and 89.01%wt gain; the rEi-EFG group had a 60.58% oocyst reduction and 56.04%wt gain. After vaccination, specific IgG levels increased and stayed high (P < 0.05). The IL-4 and IL-2 levels of rEi-EF1 alpha immunized groups showed a significant increase after immunization (P < 0.05). Both rEi-EF1 alpha and rEi-EFG could induce humoral and cellular immune responses. In contrast, rabbits immunized with rEi-EF1 alpha were better protected from challenge by E. intestinalis than rEi-EFG.