Diagnostic and control criteria for paratuberculosis are based on the assumption that all ruminant species have a similar response to the infection. However, there is some evidence that infections in each species have quite different features, like the different strains involved in cattle and sheep or variations in the pathology in each species. In order to compare the immune response in natural conditions, we designed an study involving cattle, sheep and goats comparing the effects of vaccination according to age of vaccination and paratuberculosis status of the herd. Three age cohorts (15 days, 6 months, and 1.5 to 2 years) in one farm with recorded cases of paratuberculosis and another without were tested by PPA3-ELISA, g-IFN ELISA, and blood PCR each 6 months for 1.5 years. For each age, 5-9 animals were vaccinated and 5-9 were not. Individual antibody and g-IFN ELISA results at the first control were substracted from results at subsequent controls in order to have comparable data for all species. Overall, goats had significantly (p<0.01) smaller changes in the antibody response during the period of study, while bovine had larger changes in the g-IFN response. By PCR Map was, at least, as frequently detected in PTB-free than in PTB-affected herds, both before and after vaccination. These results indicate that Map distribution might not be related to a previous clinical history of paratuberculosis in the herd, and that there are different patterns of paratuberculosis immune responses according to species, age, and clinical history.