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Control and mitigation of disease in wild ungulate populations are one of the major challenges in wildlife management. Despite the importance of the major histocompatibility complex (MHC) genes for immune response, assessment of diversity on these genes is still rare for European deer populations. Here, we conducted the first assessment of variation at the second exon of the MHC DRB in wild populations of Scottish highland red deer, the largest continuous population of red deer in Europe. Allelic diversity at these loci was high, with 25 alleles identified. Selection analyses indicated c. 22% of amino acids encoded under episodic positive selection. Patterns of MHC allelic distribution were not congruent with neutral population genetic structure (estimated with 16 nuclear microsatellite markers) in the study area, the latter showing a marked differentiation between populations located at either side of the Great Glen. This study represents a first step towards building an immunogenetic map of red deer populations across Scotland to aid future management strategies for this ecologically and economically important species.