Susac syndrome (SS) is the triad of encephalopathy, branch retinal artery occlusions (BRAOs), and hearing loss. Migraines may herald and accompany encephalopathy. Little is known about pathogenesis. Based on light microscopic findings in brain biopsy material analogous to anti-endothelial cell antibody (AECA)-mediated microvascular injury, we postulated that SS microangiopathy was attributable to AECAs. We examined serum samples from 11 patients with SS for AECAs; 9 were positive by indirect immunofluorescence and Western blot studies. A highly distinctive band on Western blots corresponding to a 50-kDa protein was observed in 8 positive SS samples; the other positive case exhibited specific reactivity with a protein band at 40 kDa. Of the 2 negative cases, 1 had been inactive since 1988; the other was an abortive variant characterized solely by BRAOs. There was enhanced surface binding of SS serum using live endothelial cell substrates compared with samples from healthy subjects. Additional serum samples from apparently healthy patients, 2 with atypical migraines, and patients with other forms of autoinflammatory disease did not show the distinctive band of immunoreactivity. SS is a distinct autoimmune endotheliopathy syndrome associated with AECAs; the antibody target seems specific in many cases and may be a disease biomarker. The exact role of AECAs in disease propagation remains unanswered.