The mannan-binding lectin (MBL)-associated serine proteases (MASPs) circulate in serum complexed with mannan-binding lectin, a recognition molecule of the complement system. MASP-2 cleaves the complement components C4 and C2 to form the C3 convertase C4b2a. A definitive natural substrate for MASP-1 has not yet been described. We investigated the substrate specifities of MASP-1 and MASP-2 using cleavage of fluorescent amide substrates by recombinant and serum-derived MASPs. Recombinant MASP-1 cleaved Phe-Gly-Arg-aminomethylcoumarin (AMC) most rapidly at a rate of 16.8 nmol min(-1) microg(-1) rMASP-1. Recombinant MASP-2 barely cleaved any of 14 substrates used. This provides means of measuring MASP-1 activity in the absence of a known natural substrate. An assay for MBL-bound MASP-1 was established using the substrate Val-Pro-Arg-AMC. Assay of MBL-bound MASP-2 was done by cleavage of a natural protein substrate, C4. The condition of the serum used for the assays is important; simulated aging showed decreased detectable MASP-1 and MASP-2 activity. The inhibitors Z-D-Phe-Pro-methoxy-propylboroglycinepinanediol ester (boroMpg), anti-thrombin III in the presence and absence of heparin, hirudin and C1 inhibitor were tested against the MASPs. C1 inhibitor inhibits both enzymes, but the protease-serpin complex is unusually unstable at alkaline pH. The thrombin inhibitor boroMpg inhibited MASP-1 but not MASP-2 while hirudin did not inhibit either protease. Anti-thrombin III alone was not inhibitory, but in the presence of heparin inhibited both MASP-1 and MASP-2. The ancient origin of MASP-1 and its thrombin-like activity suggests its involvement in a coagulation-based defense mechanism in the early evolution of innate immunity.