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Background  The major histocompatibility complex (MHC) is the most polymorphic genetic region in vertebrates, but the origin of such genetic diversity remains unresolved. Several studies have demonstrated at the  within -population level that individuals harbouring particular alleles can be less or more susceptible to malaria, but these do not allow strong generalization.    Methods  Here worldwide data on the frequencies of several hundred MHC alleles of the human leucocyte antigen (HLA) system in relation to malaria risk at the  between -population level were analysed in a phylogenetic framework, and results for different alleles were quantitatively summarized in a meta-analysis.    Results  There was an overall positive relationship between malaria pressure and the frequency of several HLA alleles indicating that allele frequencies increase in countries with strong malaria pressure. Nevertheless, considerable heterogeneity was observed across alleles, and some alleles showed a remarkable negative relationship with malaria risk. When heterogeneities were partitioned into different organization groups of the MHC, the strongest positive relationships were detected for alleles of the HLA-A and HLA-B loci, but there were also differences between MHC supertypes that constitute functionally distinct nucleotide sequences. Finally, the number of MHC alleles that are maintained within countries was also related to malaria risk.    Conclusion  Therefore, malaria represents a key selection pressure for the human MHC and has left clear evolutionary footprints on both the frequencies and the number of alleles observed in different countries.    Electronic supplementary material  The online version of this article (doi:10.1186/1475-2875-13-349) contains supplementary material, which is available to authorized users.

Global distribution of malaria-resistant MHC-HLA alleles: the number and frequencies of alleles and malaria risk