Complement is a central element of innate immune homeostasis in the human organisms. This cascade system is important to recognize and to efficiently attack infectious agents and, in addition, it also mediates the silent, non-inflammatory removal of modified autologous cells and cellular debris. A direct efficient activation of the complement cascade on the surface of infectious microbes is favorable and results in a damage and elimination of these foreign particles. At the same time, bystander host cells need maximum protection from the damaging effects of the activated system. Early in life, when the adaptive system is still evolving, the innate immune response is central for immune protection. Even slight changes in single components in form of mutations, polymorphisms, copy number variations or chromosomal rearrangements influence the balance of this central, evolutionary highly conserved immune defense network. Protective effects which are highly relevant early in life can develop to risk factors and predisposes for certain autoimmune disorders at a later age. Our work aims at defining how single disease and infection associated gene polymorphisms affect infection, the immune evasion of pathogenic microbes and cause autoimmune disorders.