To assess the contribution of the alternative pathway in complement activation and host defense and its possible role in the regulation of systemic energy balance in vivo, factor D-deficient mice were generated by gene targeting. The mutant mice have no apparent abnormality in development and their body weights are similar to those of factor D-sufficient littermates. Complement activation could not be initiated in the serum of deficient mice by the alternative pathway activators rabbit erythrocytes and zymosan. Surprisingly, injection of cobra venom factor (CVF) caused a profound and reproducible reduction in serum C3 levels, whereas, as expected, there was no C3 reduction in factor B-deficient mice treated similarly. Studies of C3 and factor B activation in vitro by CVF demonstrated that in factor D-deficient serum the ␣ chain of C3 was cleaved gradually over a period of 60 min without detectable cleavage of factor B. CVF-dependent C3 cleavage in the deficient serum required the presence of Mg 2؉ , whereas in normal mouse serum the presence of divalent cations was not required. These results suggest that in mouse proteolytic cleavage of factor B by factor D is not an absolute requirement for the zymogen to active enzyme conformational transition of CVF-bound factor B. Kinetics of opsonization of Streptococcus pneumoniae by C3 fragments was much slower in factor D-deficient serum, suggesting a significant contribution of the alternative pathway to antibacterial host defense early after infection. T he alternative pathway (AP) of complement activation is a self-amplifying mechanism important for pathogen recognition and elimination in the absence of specific antibodies. The AP also amplifies complement activation initiated by the other two pathways of complement activation, classical and lectin (1). The dual function (recognition and amplification) of the AP underlines its importance for host defense against pathogens. The proximal result of complement activation is the formation of convertases, enzymes that activate C3 and C5, generating biologically active protein fragments and complexes (1). In the AP, assembly of the C3͞C5 convertase requires the initial attachment of the C3b fragment of C3 to the surface of a pathogen and proceeds through the formation of a complex with factor B (C3bB) and the subsequent cleavage of factor B by factor D to form C3bBb, the C3͞C5 convertase of the AP.Mouse factor D was initially recognized as a serine protease encoded by a differentiation-specific message present mainly in adipocytes and cells of the nervous system (2). Because its mRNA was significantly reduced in mouse and rat models of obesity, it was thought that the protein was involved in fat metabolism (3). These observations led to naming the protein adipsin, which soon was identified with mouse factor D (4). Subsequently it was demonstrated that adipocytes also synthesize and secrete C3 and factor B, leading to the formation of a C3 convertase in culture supernatants (5). Other results indicated that C3a desArg , the ...