Recent genetic studies in multiple autoimmune and inflammatory diseases have identified hundreds of genomic loci harboring risk variants. These variants are shared between diseases at unexpectedly high rates, providing a molecular basis for the shared pathogenesis of immune-mediated disease. If properly used, these results could allow us to identify specific pathways underlying disease; explain disease heterogeneity by grouping patients by molecular causes rather than overall symptomatology; and develop more rational approaches to diagnosis and therapy targeting these molecular defects. Here we review the current state of play in the genetics of immune-mediated disease, evidence for this sharing and how this new knowledge can lead to medically actionable discoveries of pathobiology.