The MHC region contains many genes that are key regulators of both innate and adaptive immunity and is the most polymorphic in the mammalian genome. Consequently, the characterisation of the repertoire of MHC genes is critical to understanding the variation that is pivotal in determining the nature of immune responses. Currently our knowledge of the bovine MHCI repertoire is limited with only the Holstein-Friesian breed having been studied intensively. Traditional methods of MHCI genotyping are of low resolution and laborious, however next-generation sequencing (NGS) technologies have been used to enable high throughput and much higher resolution MHCI typing in a number of species. We have developed a MiSeq platform approach and requisite bioinformatics pipeline to facilitate typing of bovine MHCI repertoires. The method was validated initially on a cohort of Holstein-Friesian animals and then demonstrated to enable characterisation of MHCI repertoires in African cattle breeds, for which there was limited available data. During the course of these studies we identified >140 novel classical MHCI genes and defined 62 novel MHCI haplotypes.