The complement system is implicated among others in the clearance of apoptotic cells, and deficiency for different components of the complement system is associated with aberrant handling of apoptotic material. As a result of this, it is thought that the complement system is involved in the pathogenesis of autoimmune diseases such as systemic lupus erythematosus (SLE) which affects multiple organs. In this review, the authors highlight the available data on complement and apoptosis, as well as the role of complement in severe autoimmune diseases like SLE.