The complement system, composed of several plasma and membrane proteins, is an integral part of the innate immune system and plays a role in inflammatory response, destruction of infectious agents, elimination of immune complexes, and control of the specific (adaptive) immune response. Hereditary deficiencies of complement components are relatively rare and associated with susceptibility to a wide variety of clinical diseases. Complement components may be target of antibodies (anti-C1q, factor H, C3 alternative convertase, or C3NeF autoantibodies or anti-C1 inhibitor antibodies) that lead to acquired deficiencies. Testing the complement system is especially necessary in patients with autoimmune diseases, some kidney diseases, recurrent infections (especially meningococcal), and angioedema. Precise clinical descriptions of the phenotypes associated with these deficiencies and their molecular diagnosis are necessary to improve our understanding of the role that the complement system plays in the physiopathological mechanisms of these diseases and to propose the most specific treatment for them.