'Indigenous vaccine' prepared from 'Indian Bison Type' a native bio-type of Mycobacterium avium subspecies paratuberculosis strain 'S5' of goat origin (goat based) was evaluated in indigenous cattle herds located in gaushalas (cow shelters), endemic for Bovine Johne's disease. Cows (893) were randomly divided into vaccinated (702 = 626 adults + 76 calves) and control (191 = 173 adults + 18 calves) groups. Response to vaccination was evaluated on the basis of health (mortality, morbidity), productivity (growth rate, reproductive performance, total milk yield), immunological parameters (LTT, ELISA titer), survivability of animals naturally infected with MAP, bacterimia (by specific blood PCR), seroconversion (by indigenous ELISA) and status of shedding of MAP in feces (by microscopy) in the two groups before and after vaccination. Reduction in MAP shedding [to the extent of 100% in Herd A; and from 82.1% (0 DPV) to 10.7% (270 DPV) in Herd C] was the major finding in vaccinated cows. Whereas, the control group cows have shown no improvement. As the first indicator of vaccine efficacy, MAP bacilli disappeared from the blood circulation as early as 15 days post vaccination, however, peak titers were achieved around 90 DPV. Peak titers initially declined slightly but were maintained later throughout the study period. Control animals did not show any pattern in antibody titers. Mortality was low in vaccinated as compared to the control groups. Vaccination of endemically infected native cattle herds with inactivated whole-cell bacterin of novel 'Indian Bison Type' bio-type of goat origin strain 'S5' effectively restored health and productivity and reduced clinical BJD. Application of goat based 'indigenous vaccine' for therapeutic management of BJD in native cattle herds (gaushalas) is the first of its kind.