Organ specific autoimmunity follows induction and perpetuation of cell mediated immune effector responses to antigens expressed by somatic cells of the target organ, and clearance of persistent viral infection requires a similar immune response. Research on regulators of innate and adaptive immunity that hinder clearance of viral infection may therefore shed light on genetic factors predisposing to organ specific autoimmunity. This article discusses Ian Mackay's interests in autoimmunity when I was his assistant physician, and their influence on my group's subsequent research on persistent viral infection.