Autoimmune diseases arise from an aberrant recognition of self-epitopes by the immune system, resulting in inflammation and tissue damage. The wide range of affected organ systems and the overlap between different diseases pose several clinical challenges. Apart from establishing an accurate diagnosis, some of the problems frequently encountered are assessment of risk factors, prediction of prognosis and administration of an optimal treatment regimen. In recent years, the introduction of novel laboratory techniques have raised hopes that new answers will be provided to these challenges. In this work, we have summarized some of the prominent contributions of genetic works, microarray analyses and autoantigen microarrays to the understanding of autoimmunity and management of patients.