Proteases play several key roles in the complement system. In the classical and lectin pathways, Clr, Cls, and the MASPs are used to convert an initial recognition signal transmitted by Clq or the mannose-binding lectin, respectively, into proteolytic activity. In the same way, triggering of the alternative pathway results from acquisition of proteolytic activity by factor D. The active enzymes generated at the initial step of the three pathways are then used to produce additional proteases, the C3- and C5- convertases, that allow further amplification of the system and generation of biologically active peptides. Regulation is another facet of the role of complement proteases. In addition to factor I, which mediates proteolytic control of the formation of the C3- and C5-convertases, the regulation of factor D catalytic activity by reversible substrate/cofactor-induced conformational changes provides a self-controlled mechanism of the activation of the alternative pathway. To carry out their highly specialized functions, complement proteases have evolved unusual structural features in their serine protease domains and have acquired additional protein modules that apparently provide them with accessory binding sites for their substrates and cofactors and contribute to their extremely restricted specificity. The significant progress made in the elucidation of the structure and function of complement proteases has allowed insights into the molecular mechanisms involved in their activation and activity. This is best illustrated by the resolution of the three-dimensional structure of factor D, which provides a precise structural basis for the regulation of its catalytic activity. Although no experimental three-dimensional structure is available yet for the proteases of the C1 complex, models of their catalytic regions have been derived, which allow insights into the conformational changes occurring on Clr autoactivation and the mechanisms of substance recognition by Cls. Also, studies have provided precise information on the modules of C2 and factor B involved in the assembly of the C3-convertases. In contrast, much less information is presently available on the structure of factor I and of the MASPs. The latter enzymes also need to be fully characterized functionally. From a general point of view, however, a major difficulty in solving the structure of complement proteases arises from their relatively large size, high carbohydrate content, and modular structure, which make them refractory to crystallization and/or high-resolution X-ray diffraction analysis. Therefore, novel strategies should be designed to tackle the problem of the resolution of the three-dimensional structure of complement proteases. One possible approach commonly used for other modular proteins is to dissect them into fragments corresponding to individual modules or arrays of modules in order to solve their structure either by X-ray crystallography or by NMR and precisely identify the structural correlates of their function. This can be achieved by the production of recombinant protein fragments using the available eukaryotic or bacterial expression systems. This methodology will also allow further mapping of functionally important residues through the use of site-directed mutagenesis. Then appropriate approaches will have to be devised to reconstitute each protease from its elementary pieces, which will likely require the combined use of different techniques, including lower resolution structural techniques such as electron microscopy and low-angle solution scattering. A further and difficulty task will be to reconstruct the multimolecular proteases of complement (C1, MBL-MASP, C3- and C5-convertases) in order to get high-resolution pictures of their assembly and function. In addition to its well-established role as a major system in innate immunity, a number of studies have provided evidence for the participation of complement in the pathogenesis of disease. For example, several viruses, parasites, and bacteria have been shown to make use of membrane complement receptors to initiate cell infection (Cooper, 1998). Additional studies also provide evidence that the neurodegenerative process observed in Alzheimer's disease may result, at least in part, from direct activation of the classical pathway by the β-amyloid protein (Rogers et al., 1992). In addition, various types of inherited or acquired deficiencies of complement proteins are associated with an increased susceptibility to pyogenic infections and immune complex disease (Morgan and Walport, 1991). These considerations underline the need to develop strategies to control complement activation. Because of their high specificity, complement proteases appear to be suitable targets for this purpose. Furthermore, their strategic position at different stages of the system offers the possibility to selectively block one of the activation pathways while keeping the others working. Undoubtedly, this will require the design of highly specific inhibitors based on a thorough understanding of the structural correlates of function of complement enzymes at the atomic level.