We have previously shown that anti-dengue virus nonstructural protein 1 (anti-DENV NS1) antibodies cross-react with endothelial cells, and several autoantigens have been identified. This study shows that the antibody levels against these self-proteins are higher in sera from patients with dengue hemorrhagic fever (DHF) than those in control sera. Anti-protein disulfide isomerase (PDI) and anti-heat shock protein 60 (anti-HSP60) IgM levels correlated with both anti-endothelial cells and anti-DENV NS1 IgM titers. A cross-reactive epitope on the NS1 amino acid residues 311-330 (P311-330) had been predicted. We further found that there were higher IgM and IgG levels against P311-330 in DHF patients' sera than those in the control sera. In addition, correlations were observed between anti-PDI with anti-P311-330 IgM and IgG levels, respectively. Therefore, our results indicate that DENV NS1 P311-330 is a major epitope for cross-reactive antibodies to PDI on the endothelial cell surface, which may play an important role in DENV infection-induced autoimmunity.