Abstract: Purpose: We sought to investigate alterations in the corneal subbasal nerve plexus and endothelium in patients with Behçet’s disease (BD).Methods: This cross-sectional study included 64 patients with BD and 30 age- and gender-matched healthy control subjects. Those with BD were classified as having ocular or non-ocular disease. All subjects underwent a corneal endothelial and subbasal nerve density evaluation using in vivo confocal microscopy (IVCM). The differences among groups were analyzed using the Kruskal–Wallis test followed by Dunn’s multiple comparison procedure.Results: The mean age of study participants was 35.7 ± 10.2 years (16–58) in the ocular BD group, 39.6 ± 14.9 years (11–66) in the non-ocular BD group, and 34.1 ± 11.2 years (21–55) in the control group. No statistical significance was found in terms of age (p = 0.259) or sex (p = 0.560) between groups. The mean endothelial cell density determined with IVCM was 2124.9 ±± 417.4 cells/mm2 (1811–3275) in the ocular group and 2546 ±± 335 cells/mm2 (1798–3280) in the control group (p = 0.000). In the ocular group, the mean density of the subbasal nerve plexus was significantly lower (p = 0.004), and nerve tortuosity was significantly higher (p = 0.002).Conclusions: Ocular BD could be responsible for changes in the corneal layers, especially endothelial and corneal nerve structures. Nerve density and tortuosity differences could be inflammatory indicators for BD.