PURPOSE: To compare the thickness of the limbal epithelium (LE) and the bulbar conjunctival epithelium (BCE) between patients with dry eye disease (DED) with and without ocular graft-versus-host disease (GVHD). METHODS: This cross-sectional study enrolled 40 patients with moderate to severe DED including 20 with and 20 without chronic ocular GVHD. All patients had a comprehensive clinical ophthalmic assessment. Moreover, the thickness of the LE and BCE in both nasal and temporal regions of both eyes was measured using spectral domain optical coherence tomography. RESULTS: The average LE thickness in all patients with dry eye (GVHD and non-GVHD) was 65.8 ± 11.9 μm temporally and 69.7 ± 11.1 μm nasally (P = 0.02). The average BCE thickness was 55.8 ± 11.4 μm temporally and 60.1 ± 11.0 μm nasally (P = 0.03). There were no statistically significant differences between GVHD and non-GVHD groups in LE thickness (69.6 ± 11.7 vs. 66.1 ± 6.2 μm, respectively, P = 0.31) or BCE thickness (58.9 ± 9.6 vs. 57.3 ± 9.8 μm, respectively, P = 0.82). There was a significant correlation between LE thickness and BCE thickness (P = 0.01, Rs = 0.41). A statistically significant negative correlation was also observed between LE thickness and age (P = 0.002, Rs = -0.35). There were no significant correlations between the thickness of the LE or BCE and other clinical parameters. CONCLUSIONS: No difference exists in the thickness of the ocular surface epithelia between dry eyes with and without ocular GVHD, which would suggest that these epithelial changes may be independent of the underlying etiology and possibly only reflect the disease severity. Furthermore, there are regional variations in the thickness of the ocular surface epithelia in patients with DED.