Mannose-binding protein (MBP) plays an important role in host defense by recognizing sugar residues on certain pathogens and activating the complement cascade. Recently, we described a new protease, designated MBP-associated serine protease (MASP) which is required for complement activation by MBP. We have cloned the cDNA that encodes this protease and found that the deduced amino acid sequence contains an epidermal growth factor-like domain, two short consensus repeats and a serine protease domain. The overall structure of MASP is similar to serine proteases of the first complement component complex, C1r-C1s. Unlike C1r-C1s, however, MASP has a histidine loop structure common to many serine proteases such as trypsin and chymotrypsin. The MASP gene was mapped on the long arm of chromosome 3 which is different from C1r-C1s as well as from trypsin and chymotrypsin. These findings suggest that MASP may have emerged prior to C1r-C1s from a common ancestor. This implies that MBP-MASP, a complex of lectin and serine protease, presumably evolved prior to adaptive immune recognition involving antibody and the classical complement pathway.