Deficiency of an early component of the classical complement pathway, C1q, C1r/C1s, C4, or C2, regularly produces autoimmunity in man, especially systemic lupus erythematosus. It has long been suggested that disruption of this pathway would lead to the inappropriate handling of immune complexes. An intriguing hypothesis that builds on this idea relates to a defect in clearance of one's own cellular debris, namely apoptotic cells. An attractive feature of this emerging concept is that blebs on apoptotic cells are decorated with antigens to which much of the autoantibody specificity is directed in systemic lupus erythematosus. A second hypothesis, generated primarily from complement deficiencies, relates to an impairment in the humoral immune response or in the regulation of autoreactive B cells. This review begins by summarizing the recognized autoimmune manifestations of complement deficiency and then describes new data derived from targeted gene deletions of complement proteins.