Technology has advanced to the stage where it is now possible to identify genes that confer low to moderate risk of developing autoimmune diseases such as rheumatoid arthritis (RA). This has been facilitated by the growing appreciation that these hard to detect genetic signals can only be defined in large cohorts of well characterized patients. In RA, the association between disease susceptibility and genes encoded within the MHC has been known for decades. Recent studies have identified several new candidate genes that provide further insights into the molecular nature of aberrant immune responses in chronic inflammatory diseases. Here, we describe some of these new genes. Based on their known functions we propose that in a subgroup of patients with RA inheritance of allelic variants at distinct loci could lead to dysregulation of adaptive immune responses characterized by chronic, low-amplitude signaling transduced by antigen T cell receptors.