Control of paratuberculosis by fecal culture and culling is expensive and has not fully answered to its theoretical potential. Although vaccination is not expected to lead to rapid eradication of the infection, it might be the most practical approach to stop losses and to decrease transmission in the short term. In this study, we have analyzed some indicators of the effects of vaccination in a field trial where an experimental vaccine was applied in a heavily infected herd. Indirect ELISA, IFN-γ, and blood PCR were carried out every six months during one and a half year in a cohort of 21 dairy cattle in a heavily affected herd. Fecal culture and PCR were additionally used at the beginning and the end of the follow-up. Finally, 12 vaccinated and 9 non-vaccinated animals were killed and samples from the intestine and enteric lymph nodes were cultured for isolation of Map. Only two fecal cultures from the non-vaccinated group were positive at the end of the follow-up. Fecal PCR was positive in 3 vaccinated and in 3 non-vaccinated animals at the last control. Blood PCR showed a similar proportion of positive results among vaccinated and non-vaccinated cattle. All vaccinated and non-vaccinated cattle had high humoral and cellular immune responses that were probably related to limited differences in the response associated to vaccination. However, there was a significantly lower proportion of tissue culture positive animals in the vaccinated group. Infected animals, including a vaccinated one, showed a decreased immune response compared with their non-infected mates. These results suggest there was a strong background of immune stimulation in this affected herd which did not allow to clearly see the immune effects of vaccination. However, the vaccine used showed a strong effect in terms of infection protection.