Background/Purpose: Juvenile dermatomyositis (JDM) is a systemic disorder of childhood characterized by muscle inflammation and vasculopathy. The mechanisms of the blood vessel injury in JDM remain to be fully solved. Anti-endothelial cell antibodies (AECA) are detected in infectious, inflammatory diseases and autoimmune diseases such as vasculitis, and we have hypothesized that such antibodies may target the endothelium in JDM. In this study, we aimed to comprehensively detect endothelial target antigens in JDM using a proteomics approach. Methods: We extracted proteins from human aortic endothelial cells (HAEC), which were used as antigen sources. To comprehensively detect target antigens for AECA, we separated proteins extracted from HAEC by two-dimensional electrophoresis (2DE) and then transferred them onto membranes. Using standard western blotting techniques, membranes were probed with sera from children with JDM or healthy controls. Autoantigens that were positive only in sera from children with JDM but not healthy controls were then identified by mass spectrometry (MS). Enzyme-linked immunosorbent assay (ELISA) was then used to confirm presence of specific antibodies. Results: Five candidate protein spots as JDM-specific proteins were detected in 2DE-WB. From these spots, we successfully identified 34 proteins. 22 of the 34 identified antigens represented membrane proteins. Using Ingenuity Pathway Analysis, 27 of the 34 candidate target antigens for AECA in JDM were predicted to interact with chaperone proteins involved in antigen processing and presentation. Among the 8 chaperone or co-chaperone proteins were heat shock cognate 71 kDa protein (HSC70), heat shock protein HSP 90-beta (HS90B) and stress-induced-phosphoprotein 1 (STIP1), a protein that mediates the association of HSC70 and HSP90. By ELISA, IgG autoantibodies to HSC70 were detected in 23% of the patients with JDM (n=39). However, 50% of the untreated JDM patients with active disease (n=10) had anti-HSC70 antibodies, in contrast to 7% (p<0.05) of the patients with juvenile idiopathic arthritis (JIA) (n=15) and 5% (p<0.01) of control children (n=20). 13% of the treated JDM patients with active disease (n=15) and 14% of the inactive patients with JDM (n=14) had anti-HSC70 antibodies. IgG autoantibodies to HS90B were detected in 6% of the patients with JDM (n=31) and in 5% of control children, in contrast to 20% of the patients with JIA. Similarly, IgG autoantibodies to STIP1 were not detected patients with JDM, but were present in 5% of control children and 20% of the patients with JIA. Conclusion: IgG antibodies to chaperone proteins in the proteome of HAEC are present in the sera of children with JDM. The presence of AECA in JDM could implicate these antibodies in the disorders of immune system in JDM.