The impact of natural infection with Babesia bovis on the immune response to FMD vaccine in caves was studied. Three groups of calves, group (1) were Babesia bovis free and vaccinated with inactivated FMD vaccine, group (2) naturally Babesia bovis infected and vaccinated with inactivated FMD vaccine, while group (3) was kept as non infection non vaccinated control, The humoral immune response of each group was measured by scrum neutralization test (SNT) for a period of 16 weeks. Babesia bovis naturally infected group of calves (gp. 2) showed tendency of lower antibody responses in comparison with uninfected (gp. 1) post vaccination with Foot and Mouth Disease (FMD) vaccine. Parasitemia of B.bovis infected calves were ranged from 1.5% to 2.5% at time of vaccination accompanied with reduction in pecked cell volumes (PCV) up to 23% less than control group. The parasite persisted in the blood of infected calves as carriers with low parasitemia. Three isolates of B.bovis have been identified. Protein characterization of the three isolates of B.bovis immunogens resulting in immunosuppressive effect was investigated. The isolates identified and propagated in cell culture using microaerophiles stationary phase and characterized by sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) and Western immunoblot. The molecular weights of antigens were varied froml2 to 1648 Kilo Daltons (KDa). The isolates showed totally 30 polypeptide antigens. Nineteen antigens were detected as homologous and common between the isolates, their molecular weights were 160, 152, 132, 110, 85, 77, 70. 67. 60, 49, 45, 40, 39, 35, 33, 30, 23, 18 and 12 KDa While the other {1 antigenic band were detected as heterologous and differ between the isolates. Their molecular weights were 165, 155, 153, 144, 140, 120, 112, 62, 37 and 20 KDa. Isolates no.1, 2 and 3 contained 24, 28 and 24 out of the 30 immunogens respectively. The immune suppressive titers of B.bovis infected calves might be due to one or more of B.bovis common antigens.