This research focuses on the role of HLA in disease associations and drug development. HLA is the most polymorphic region of the human genome, hence the high sequencing capacity of Next Generation Sequencing has brought new possibilities to discover and resolve its complexity. As the HLA alleles are highly homologous the sequencing is a very challenging task, and the whole HLA community has to adopt themselves to the new era of technology before accept and use the results of the Next Generation Sequencing. As the number of discovered sequences and novel alleles are increasing together with the throughput and resolution the NGS is able to provide it is important to re-consider the role of HLA alleles in certain disease associations and drug discovery in terms of how the sequence and the difference in the sequence of individual alleles influence the structure of the proteins that have role in the human immune system. I aim to give a full introduction to the HLA world. As this is a special and hardly documented region of the genome, a lot of research excluded the examination of HLA earlier. Thereby special experiments and methods were born to assist researchers to understand the structure and role of the HLA.