The human leukocyte antigens (HLA) are highly polymorphic cell surface proteins encoded in the major histocompatibility complex (MHC) region on chromosome 6. The HLA system has been well known as transplantation antigens but the primary biological role of the HLA molecules is regulation of immune response by presenting peptide fragments to T-lymphocytes. As regulators of immune responses the HLA molecules are also of importance for susceptibility to several autoimmune and inflammatory diseases. Genotyping of these loci is therefore significant in research targeting the mechanisms of HLA associated diseases, in exploring new epidemiological associations between HLA and specific disease, and as a clinical tool for risk assessment for diseases with well defined associations. Although several commercial HLA genotyping methods are available, many require multiple steps, have low throughput and high cost. The aim of the work within this dissertation was to develop a robust, costeffective method for HLA-DRB1, -DQA1 and -DQB1 genotyping suitable for use in an epidemiological context and clinical investigation. The method was optimized with specific focus on risk alleles for type 1 diabetes mellitus and celiac disease, two autoimmune disorders with significant impact on public health. By combining PCR with sequence specific primers (PCR-SSP), product separation by capillary gel electrophoresis and fluorescence detection in the developed method, all three loci could be analyzed in a single step, resulting in low reagent cost and fast turnaround time. This in combination with the low total consumption of DNA template allows the method to be used in epidemiological studies. 10 A simplified version of the developed method is currently used for clinical risk assessment for celiac disease when histological and/or serologic results are ambiguous in investigated subjects or when a gluten-free diet has been initiated before diagnostic tests have been performed. The low cost of this newly developed method has enabled HLA typing as a tool in screening programs for high-risk groups, such as individuals with Down syndrome or type 1 diabetes, to preclude the risk for celiac disease and thus avoid periodic screening for auto-antibodies. This method is also used to analyze samples from children all over Sweden with newly diagnosed diabetes in the Better Diabetes Diagnosis project. The developed method was also used in two explorative association studies not related to type 1 diabetes or celiac disease. In one study the association between HLA-DRB1, -DQA1 and -DQB1 and acute myocardial infarction was investigated showing only weak associations. In the second study the HLA-DR-DQ haplotype effect on developing chronic pain after inguinal hernia surgery was explored demonstrating an HLA dependent risk of developing pain