Mutations and polymorphisms in the regulator of complement activation, factor H, have been linked to atypical hemolytic uremic syndrome (aHUS), membranoproliferative glomerulonephritis, and age-related macular degeneration. Many aHUS patients carry mutations in the two C-terminal modules of factor H, which normally confer upon this abundant 155-kDa plasma glycoprotein its ability to selectively bind self-surfaces and prevent them from inappropriately triggering the complement cascade via the alternative pathway. In the current study, the three-dimensional solution structure of the C-terminal module pair of factor H has been determined. A binding site for a fully sulfated heparin-derived tetrasaccharide has been delineated using chemical shift mapping and the C3d/C3b-binding site inferred from sequence comparisons and computational docking. The resultant information allows assessment of the likely consequences of aHUS-associated amino acid substitutions in this critical region of factor H. It is striking that, excepting those likely to perturb the three-dimensional structure, aHUS-associated missense mutations congregate in the polyanionbinding site delineated in this study, thus potentially disrupting a vital mechanism for control of complement on self-surfaces in the microvasculature of the kidney. It is intriguing that a single nucleotide polymorphism predisposing to age-related macular degeneration occupies another region of factor H that harbors a polyanionbinding site.Inappropriate or disproportionate activation of the complement system underlies the debilitating symptoms of a long list of autoimmune, degenerative, and iatrogenic diseases (1). The role of the complement system is to rid the body of infectious agents and clear the bloodstream of immune complexes, apoptotic cells, and other debris (2, 3). Following its activation, deposition of complement proteins onto target surfaces ensues, marking the target for destruction and clearance, accompanied by release of mediators of inflammation and activators of the acquired immune response. Tight regulation and targeting of the complement system is thus essential to good health. The recent association of genetic variations in complement regulatory proteins with pathologies of the kidney (4, 5) and eye (6 -9) is an important development. It not only offers additional insights into the role played by complement in pathophysiological mechanisms, but it opens up the possibility of tailoring prevention and intervention according to genotype. The ability to consider such sequence variations within the context of a three-dimensional structure in which key functional regions have been identified significantly enhances these opportunities. In this report, we describe the structure of a region of factor H implicated in atypical hemolytic uremic syndrome (HUS).