The complement system can be activated by one of three pathways (classical, lectin and alternative) and provides important host defense, homeostasis and immune regulatory functions. However, the complement system also plays a pathogenic role in many autoimmune and inflammatory diseases, including systemic lupus erythematosus (SLE or lupus) (1). Systemic lupus erythematosus is the prototypic human autoimmune disease, and complement mediated injury is initiated by immune complexes (IC) formed by autoantibodies directed against a broad range of self-antigens (2, 3). The kidney is a major site of immune complex formation and/or deposition, and lupus nephritis is a major cause of morbidity and mortality, both in human SLE and in murine models. There is, however, an apparent dual role for complement in the development and progression of lupus, highlighted by the different roles of the classical and alternative complement pathways in the disease. Patients with homozygous deficiencies of early components of the classical pathway, such as C1 (C1q or C1r/s) or C4, have an increased incidence of lupus and lupus-like disease (>80%) (1, 4). On the other hand, homozygous deficiencies of C3, a protein that plays a pivotal role in all three complement activation pathways, is associated with membranoproliferative glomerulonephritis (5), but only rarely lupus (6). Studies in murine models also show a link between the classical pathway and autoimmune disease. Mice deficient in C1q have increased mortality and higher titers of autoantibodies, with 25% of C1q deficient mice developing glomerulonephritis with glomerular IC deposits and multiple apoptotic bodies (7). C1q and C4 deficiency are also associated with the development/acceleration of lupus-like disease in mice on an autoimmune background (8, 9), and C1q−/− and C4−/− mice (on 129/Sv × C57BL/6 background) exhibit an impaired ability to clear apoptotic cell bodies. Together, these data are consistent with the hypothesis that the classical pathway provides a protective role in the development of lupus via its role in the clearance of apoptotic cells that otherwise provide a source of autoantigens to fuel the disease process (10), although other hypotheses have been proposed (11). In contrast to the protective role of the classical pathway, there is strong evidence that the alternative pathway plays a key role in the development of lupus. MRL/lpr mice spontaneously develop an autoimmune syndrome similar to human SLE (12), and MRL/lpr mice deficient in either of the alternative pathway proteins fB or fD, are protected from renal disease (13, 14). In addition, various complement inhibitors are protective in murine models of lupus. Recombinant soluble forms of the mouse C3 inhibitor, Crry, provided protection against renal injury in MRL/lpr mice. These inhibitors, Crry-Ig (15), and CR2-Crry (16), also provided protection against skin/ear lesions and glomerular deposition of IC’s and C3. However, only the targeted inhibitor, CR2-Crry, reduced glomerular inflammation, mortality and autoantibody levels, and there were significantly increased levels of circulating IC in MRL/lpr mice treated with Crry-Ig compared to mice treated with CR2-Crry. These effects of CR2-Crry were observed in mice treated once a week with the inhibitor. These different outcomes may be related to the systemic vs. localized nature of complement inhibition by Crry-Ig and CR2-Crry, respectively. The CR2 moiety of the CR2-Crry fusion protein targets to iC3b, C3dg and C3d, cell-bound activation fragments of C3 that are deposited at sites of complement activation. Complement inhibition with an anti-C5 monoclonal antibody is also protective in the NZB/NZW F1 model of lupus (17). Significantly, however, whereas C3 inhibition and alternative pathway deficiency is protective in MRL/lpr mice, C3 deficiency is not. In fact, there is earlier and significantly greater albuminuria and increased glomerular IgG deposition in the C3−/− MRL/lpr mice compared to C3+/+ controls (18). Thus, total blockade of all complement pathways (as opposed to temporary and/or targeted blockade with inhibitors) was not protective and appeared to exacerbate disease. Collectively, the above studies suggest that selective inhibition of the alternative pathway will provide an effective therapeutic strategy for lupus, and that a targeted approach to complement inhibition has the potential to provide additional benefit with less immune suppression and toxicity. Here we report on the characterization of CR2-fH, a recently described targeted complement inhibitor that is specific for the alternative pathway, in treatment of disease in the MRL/lpr model of lupus. For clinical relevancy, treatment was begun after the onset of renal disease, and the effect of CR2-fH on immune modulation and disease progression was compared to the effect of CR2-Crry, an inhibitor of all complement pathways.