The complement system is an important factor in innate immunity. The third complement component, C3, is central to the classical, alternative and lectin pathways of complement activation. Activation products of the complement cascade contain neo-epitopes that are not present in the individual native components. The synthesis of C3 is tissue-specific and is modulated in response to a variety of stimulatory agents. C3 is the most abundant protein of the complement system with serum protein levels of about 1.3mg/ml. An inherited deficiency of C3 predisposes the person to frequent bacterial infections. C3 fragments are deposited in tissues at sites of antibody-mediated immunopathology. In ulcerative colitis and idiopathic chronic inflammatory bowel disease, the deposition of C3 in the diseased mucosa has been reported. Proteolysis by C3-convertases results in the cleavage of C3 into C3a and C3b. C3b becomes attached to immune complexes and is further cleaved into iC3b and C3f. iC3b is further processed into C3c and C3dg.