Recently, we described changes in lymphocyte distribution and function, total and specific mRNA expression in gut-associated lymphoid tissue (GALT) of neonatal lambs experimentally infected with a cervine strain of Mycobacterium avium subspecies paratuberculosis (Map). In this study, a similar protocol was used to assess immune events in vaccinated and non-vaccinated lambs, and to compare responses between animals infected with cervine or ovine isolates of Map. Five groups of five lambs were treated as follows: A) Non-infected/non-vaccinated (NINV); B) Non-infected/vaccinated (CVL, Weybridge Johne's disease vaccine) (NIV); C) Infected (cervine isolate)/non-vaccinated (CINV); D) Infected (cervine isolate)/vaccinated (CIV); E) Infected (ovine isolate)/non-vaccinated (OINV). Findings in A and B were comparable to those from the original experiment: circulating IgG and GALT B cell numbers were significantly (p<0.05) decreased and GALT T/B cell ratios increased. Vaccination and/or infection with the ovine strain had a significant (p<0.05 by ANOVA) impact on both lymphocyte and Ig distribution. The relevance of these early immune changes and their regulation in terms of disease development is under further investigation.