Antiendothelial cell antibodies (AECAs) have been detected in patients who have autoimmune and inflammatory diseases. Previous studies showed that AECAs against human umbilical vein endothelial cells were detected in healthy subjects. In the present study, we evaluated AECAs against human brain microvascular endothelial cells (HBMEC) in serum. We detected 250 antigen spots that reacted with AECAs in serum samples from 30 healthy subjects by 2-dimensional immunoblot using primary cultured HBMEC as the antigen source. There were 10 spots that corresponded to common target antigen spots and reacted with AECAs in serum samples from > 25% of the 30 healthy subjects. We identified 7 proteins that corresponded to 8 of the 10 spots by mass spectrometry: 78-kDa glucose-regulated protein, dihydropyrimidinase-related protein 2, heterogeneous nuclear ribonucleoprotein L, vimentin, perilipin 3, alpha-enolase, and annexin A2. The results suggest that these 7 HBMEC proteins are major target antigens of natural AECAs.