The past few years have seen the identification of PTPN22 and the confirmation of CTLA-4 as common autoimmune disease genes. Together with MHC and INS, these developments have increased the collection of confirmed susceptibility loci for autoimmunity. In this article, the latest developments related to these genes and to other recently studied candidate autoimmune susceptibility loci (PDCD1, FCRL3, SUMO4, CD25, PADI4 and SLC22A4) are reviewed. Collectively, these genes strongly indicate that aberrant inhibition of the signalling cascade initiated by activation of the T-cell receptor is involved in the aetiology of autoimmune disease. However, much basic genetic, molecular and clinical research is still needed to help us fully understand the underlying mechanisms of autoimmunity and how these translate into prognosis or therapy.