Activation of the complement system by the classical, mannan binding lectic (MBL) or alternative pathway results in the generation of multiple complement proteolytic cleavage products, recruited from these inactive precursor molecules in a sequentially proceeding cascade (Chapter 1). This leads to an alteration of their antigenic pattern and thus to the consumption of the nativemolecule. Concomitantly, complement activation initiates formation of multi-molecular complexes such as the C3 or C5 convertases or the terminal complement complex (TCC). The latter can be generated on biological membranes or in the fluid phase (C5b-9). Activation-dependent changes on molecules or complexes can be revealed by the disappearance of native-restricted epitopes, and by the appearance of neoepitopes (1), and are usually assessed by means of monoclonal antibodies in enzyme-linked immunosorbent acids (ELISAs). This chapter focuses on the sensitive and specific quantitation of (native) complement proteins to evaluate the inactivated (background) status, and also on that of their fragments and complexes to reliably assess complement activation in vivo, with particular respect to neoepitopes of C9 appearing only when C9 is incorporated into the terminal complement complex.