C2 and Factor B are heat-labile β-globulins in normal human serum and are the precursors of the C3 and C5 convertase enzymes of the classical and alternative complement pathways, respectively. Genes controlling C2-deficiency and polymorphism and Factor B polymorphism have been linked to the HLA locus. In this study, proteolysis of C2 and Factor B have been compared by a peptide mapping technique on SDS polyacrylamide gel electrophoresis. C2 and Factor B were purified from the 20% Na2SO4 supernatant of human plasma by sequential column chromatography and by preparative gel electrophoresis in barbital-glycine buffer, pH 8.8. The highly purified C2 and Factor B sedimented at 5.2S and 5.0S, respectively, and were hemolytically and esterolytically active. The m.w. for C2 and Factor B estimated by SDS polyacrylamide gel electrophoresis in the presence or absence of reducing agents were 117,000 and 93,000 daltons, respectively, suggesting that each protein is comprised of a single polypeptide chain.