M.a. paratuberculosis is the causal agent of paratuberculosis (Johne's disease). Recent work has suggested that gamma delta T cells may play an important role in the early immunological response to mycobacterial diseases, and that CD1 may act as a non-classical MHC molecule in antigen presentation to these gamma delta T cells. Experimental infection of neonatal lambs with M.a. paratuberculosis was used to investigate the changes in gamma delta T cells and CD1 molecules in the gut associated lymphoid tissue 4 weeks after inoculation. Immunohistochemistry was used to label the gamma delta lymphocytes and CD1 molecules. An increase in the number of gamma delta T cells was noted in both the jejunal and ileal Peyer's patches in the gut of infected lambs, but no statistically significant change was found in the mesenteric lymph nodes. There were no obvious changes in the CD1 molecules in any tissue. This work suggests that gamma delta T cells may play a role in the initial immunological events of paratuberculosis infection.