Major histocompatibility complex (MHC) variation at the class IIβ (B-LB) gene was surveyed both within and among populations of red grouse Lagopus lagopus scoticus from northeastern Scotland. Variation among individuals was assayed by direct DNA sequencing, with 13 unique alleles being resolved among 10 unrelated individuals. All nucleotide substitutions were non-synonymous (amino acid changing) substitutions. Variation among five populations was screened using single stranded conformational polymorphism (SSCP). Twelve B-LB alleles were resolved, with low levels of genetic structure between the populations. This is in contrast to the considerable genetic differentiation observed among the same populations determined from microsatellite DNA analysis. Both the patterns of nucleotide substitution within individuals, and the discrepancy between MHC and microsatellite derived patterns of population genetic structure highlight that balancing selection is acting to maintain variation in the grouse MHC. The significance of MHC dynamics and diversity is discussed in the context of grouse ecology and conservation.