Purpose. Recently, mutations in the M1S1 gene have been identified as responsible for gelatinous drop-like corneal dystrophy (GDLD). How the abnormal M1S1 gene product causes GDLD is not known, although evidence suggests that it may compromise corneal epithelial function. This investigation attempted to determine the effect of the abnormal M1S1 gene product by assessing epithelial barrier function and epithelial ultrastructure in GDLD corneas. Methods. Epithelial barrier function was assessed on the basis of fluorescein uptake. The method used a modified slit-lamp fluorophotometer. High-resolution scanning electron and atomic force microscopy was used to investigate the amyloid deposits and epithelial cell structure. Results. Epithelial permeability was orders of magnitude higher in GDLD corneas than normal. The structure of the amyloid deposits was characterized, and clear abnormalities in epithelial morphology and cell junctions were observed. Conclusions. The high epithelial permeability observed in GDLD corneas was directly correlated with abnormalities in epithelial structure, including irregular cell junctions. This suggests that the abnormal M1S1 gene product may affect epithelial cell junctions resulting in increased cell permeability in GDLD corneas.