CD8 T cells specific for parasitized cells have been shown to be key mediators of immunity to Theileria parva. The CD8 T cell responses are frequently parasite strain-restricted and strain specificity correlates with lack of cross protection between different parasite strains. A number of T. parva antigens have now been identified using parasite-specific CD8 T cell lines as screening reagents. Published data on two of these antigens (Tp1 and Tp2) has revealed sequence polymorphism, which was particularly extensive in parasites isolated from African buffalo (Syncerus caffer), an important wildlife reservoir of T. parva. The current study set out to further investigate sequence diversity in naturally infected buffalo by applying high throughput (Roche 454) sequencing to PCR amplicons of a panel of 6 antigen-encoding genes obtained from Kenyan and South African buffalo. This approach yielded large numbers of sequence reads for each gene. Overall, the number of variant nucleotide sequences detected for each gene ranged from 29 to 76. Single blood samples from individual animals also contained multiple sequence variants, with up to 19 alleles of one gene detected per animal. Principal co-ordinate analysis did not reveal any meaningful sub-clustering based on their geographical origin, indicating that much of the evolution of diversity in these genes occurred prior to geographical separation. Analysis of translated amino acid sequences, confirmed the previous finding of extensive sequence diversity in the Tp1 and Tp2 antigens (>60 variants of each). By contrast, the remaining 4 antigens showed a high level of conservation in their amino acid sequences, with few or no amino acid substitutions. Preliminary analyses of CD8 T cell responses in immune cattle indicate that responses to these conserved antigens represent a minor component of the response and that strain specificity is dictated by highly dominant responses to the polymorphic antigens.