Autoimmune diseases are known to have a multifactorial pathogenesis, with both environmental and inherited components. Wide technical progresses together with the completion of the sequencing of human genome have recently allowed the identification of new genetic risk variants in many autoimmune disorders. While part of these studies confirmed previous knowledge, most of the data has disclosed novel and unsuspected roles in the development of autoimmunity for molecules involved in various pathogenic pathways. After the current first wave of data from high-density genome-wide studies, we now need to further characterize these genetic factors and find additional ones, possibly among rare variants. In addition, a role for sex chromosomes in the development of autoimmune diseases has also been suggested. This review will focus on the recent discoveries related to genetics of autoimmunity.