Efforts to understand autoimmunity have been pursued relentlessly for several decades. It has become apparent that the immune system evolved multiple mechanisms for controlling self-reactivity, and defects in one or more of these mechanisms can lead to breakdown of tolerance. Among the multitude of lesions associated with disease, the most common appear to affect peripheral rather than central tolerance. The initial trigger for both systemic and organ-specific autoimmune disorders likely involves recognition of self or foreign molecules, especially nucleic acids, by innate sensors. This recognition, in turn, triggers inflammatory responses and engagement of previously quiescent autoreactive T and B cells. Here, we summarize the most prominent autoimmune pathways and identify key issues that require resolution to fully understand pathogenic autoimmunity.