Few countries using vaccines have effectively decreased incidence of clinical JD. In this study efficacy of indigenous inactivated vaccine containing highly virulent field strain of Mycobacterium avium subspecies paratuberculosis (MAP) 'Bison type' was compared with 'Commercial Inactivated Vaccine' for the recovery from clinical JD in naturally infected goats. A total of 71 adult, weak, infected (culture and sero-positive), ready to cull goats belonging to farm units of Central Institute for Research on Goats (CIRG), Makhdoom (endemic for JD), were randomly divided into 3 groups. 'Group- A' of Indigenous vaccine, 'Group- B' of Commercial vaccine and 'Group- C' of Sham Immunized' controls. After vaccination, physical condition, body weight gained, fecal shedding of MAP, humoral and cell-mediated immune responses, mortality and morbidity etc., were monitored for 7 months. At the end of trial there was marked overall improvement in body condition of the vaccinated animals (Group A and B) as compared to 'Group-C'. Body coat showed marked improvement in shining, pliability, smoothness, regained luster and re-generation of hairs. Many of the goats kidded, delivering healthy kids and marked improvement in milk production. Average body weights gained per animal were significantly high (p<0.05) in the goats of Group-A as compared to Group B and C. Mortality and morbidity rates (due to diarrhea, weakness and Johne's disease) were lower in 'Group-A' goats as compared to 'Group-B' and 'Group-C' goats. Gross lesions in goats died and necropsied from vaccinated groups (Group A and B) during the study showed regression of lesions of JD and regeneration of fat, while 'Sham immunized' goats had frank lesions of JD. Lymphocyte transformation test (LTT) (indicator of cellular response) showed higher stimulation of PBMCs in 'Group-A' animals with MAP antigen as compared to PBMCs in 'Group-B' and 'Group-C' goats. Concentration of nitric oxide, (cellular response), was also higher in 'Group-A' goats followed by 'Group-B' and 'Group-C'. Goats of both vaccinated groups also had higher protective antibody titer in comparison to 'Sham-immunized' goats. Both the vaccines reduced fecal shedding remarkably but indigenous 'Bison type' vaccine was more effective. However, few of the very advance cases of Johne's disease did not recover and died eventually during the study and at necropsy had frank lesions of JD. Overall both the vaccines were effective in restricting MAP infection and JD in clinically infected goats but indigenous vaccine using native MAP 'Bison type' strain of goat origin was superior.