The genes of the major histocompatibility complex (Mhc) are known to be highly polymorphic in songbirds, in part due to gene duplication. The Mhc class I exon 3 of the house sparrow (Passer domesticus) is investigated in this study as it has been characterized previously. We expected nextgeneration sequencing to enable Mhc genotyping to be achieved more accurately than traditional methods with lower resolution. We first compared genotyping performance of two next-generation sequencing techniques (454 amplicon and Illumina MiSeq sequencing). Illumina MiSeq sequencing was more successful than 454 amplicon sequencing when sequencing individuals with a high number of Mhc alleles because of the higher readdepth coverage that could be achieved. Pathogens are thought to maintain the high polymorphism at Mhc. We investigated the pattern of differentiation at the Mhc in relation to differences in the prevalence and infection with Plasmodium, also assessed using newgeneration sequencing, in multiple house sparrow populations in New Zealand. The study provided evidence for geographical differentiation at the Mhc class I in New Zealand. There was no evidence of a relationship, however, between Mhc diversity and Plasmodium infection. Studies on Mhc-related fitness have found a relationship between Mhc diversity and fitness traits, such as reproductive fitness and survival. Moreover, empirical evidence has suggested an association between specific Mhc alleles and fitness traits. We therefore examined the fitness consequences (reproductive fitness and survival) of Mhc across cohorts within an intensively monitored long-term study of a house sparrow population on Lundy Island. We found two Mhc alleles to be associated with reproductive fitness (number of offspring produced in their lifetime).