Activated Factor B, incorporated into the cobra venom factor (CVF)-dependent C3/C5 convertase, was inactivated by diisopropylfluorophosphate (DFP). Inactivation was time- and dose-dependent and was enhanced by the presence of substrate. Treatment of the zymogen of Factor B with DFP effected significant inactivation. Incorporation of [3H]diisopropylphosphate into the zymogen and into the activated form of Factor B was demonstrated after [3H]DFP treatment and subsequent electrophoresis of the proteins on polyacrylamide gels containing sodium dodecyl sulfate. Inactivation of activated C2 incorporated into the classical C5 convertase was observed on DFP treatment of the enzyme. DFP also reduced the activity of the C2 zymogen. The description of their serine proteinase nature further emphasizes the close structural and functional relationship of C2 and Factor B.