The adaptive immune system augments host defenses against diverse infectious threats, yet also carries intertwined risks for the development of autoimmune disease. The immune system incorporates homeostatic pathways for essential housekeeping functions that involve recognition of oxidation-modified endogenous molecules. Now, the properties of a physiological class of natural autoantibodies, which seem to modulate the severity or even prevent the onset of autoimmune disease, are beginning to be defined. Whereas disease-associated IgG autoantibodies to nuclear antigens and citrulline-modified self-proteins have been shown to activate innate pattern recognition receptors leading to increased cell death and tissue injury, a class of IgM autoantibodies to oxidation-associated neo-antigens can oppose these pathogenic effects. These naturally arising regulatory IgM autoantibodies enhance the capacity for the phagocytic clearance of host cells affected by programmed death pathways. These antibodies can also suppress key signalling pathways in the innate immune system involved in the control and resolution of inflammatory responses to Toll-like receptor agonists and disease-associated IgG autoantibodies.