Autoimmune uveitis and posterior scleritis are ocular diseases caused by immune dysregulation. Their pathogenesis remains elusive, and delayed diagnosis can exacerbate vision loss. Our study analyzed proteomic profiles of 190 patients with Behçet’s disease uveitis, posterior scleritis, and Vogt-Koyanagi-Harada syndrome. Bioinformatics methods revealed potential pathogenesis and biomarkers for the diseases, which were verified by enzyme-linked immunosorbent assay.