Self-reactive natural antibodies initiate injury following ischemia and reperfusion of certain tissues, but their role in ischemic stroke is unknown. We investigated neoepitope expression in the post-ischemic brain, and the role of natural antibodies in recognizing these epitopes and mediating complement-dependent injury. A novel IgM mAb recognizing a subset of phospholipids (C2) and a previously characterized anti-annexin IV mAb (B4) were used to reconstitute and characterize injury in antibody deficient Rag1â/â mice after 60 minutes of middle cerebral artery occlusion and reperfusion. Reconstitution with C2 or B4 mAb in otherwise protected Rag1â/â mice restored injury to that seen in wild-type mice, as demonstrated by infarct volume, demyelination and neurological scoring. IgM deposition was demonstrated in both wild-type mice and reconstituted Rag1â/â mice, and IgM co-localized with the complement activation fragment, C3d, following B4 mAb reconstitution. Further, recombinant annexin IV significantly reduced infarct volumes in wild-type mice and in Rag1â/â mice administered normal mouse serum, demonstrating that a single antibody reactivity is sufficient to develop cerebral ischemia reperfusion injury in the context of an entire natural antibody repertoire. Finally, C2 and B4 mAbs bound to hypoxic, but not normoxic, human endothelial cells in vitro. Thus, the binding of pathogenic natural IgM to post-ischemic neoepitopes initiates complement-dependent injury following murine cerebral ischemia and reperfusion and, based also on previous data investigating IgM reactivity in human serum, there appears to be a similar recognition system in both mouse and man.