Despite the low numbers of MAIT cells in mice, MAIT cells have been found to have a non-redundant role in vivo in the control of bacterial infections, including with Mycobacterium species. Johne’s disease in deer is caused by Mycobacterium avium subsp. paratuberculosis and presents as a chronic inflammatory disease of the gastrointestinal tract. We have bred lines of red deer (Cervus elaphus) that display susceptibility or resilience to Johne’s disease, although the mechanism for this phenotype is not fully understood. Using real time PCR, we have characterised the abundance of MAIT cells (Vα19.2-Jα33) in different tissues from resilient and susceptible red deer infected with M. avium subsp. paratuberculosis. No difference in MAIT cell frequency was seen between groups across a range of intestinal and extra-intestinal tissues. However, the abundance of MAIT cells differed significantly between tissues, with Vα19.2-Jα33 transcripts highest in the liver. These results argue against a role for MAIT cells in the resilience phenotype to Johne's disease.