Purpose: To study the corneal endothelial morphological changes and endothelial barrier function in contact lens wearers. Methods: Specular microscopy and anterior segment fluorophotometry were performed on 116 controls (group 1) and 76 daily wear soft contact lens wearers. Group 2 patients (n = 34) had been wearing contact lenses for less than 5 years and group 3 (n = 42) for more than 5 years. The relationship of corneal thickness, endothelial cell density, hexagonal cell percentage, coefficient of variation in cell area, corneal autofluorescence and corneal endothelial permeability to the contact lens wear duration was studied. Results: The average corneal thickness of contact lens wearers did not differ significantly from controls (0.533 ± 0.031, 0.538 ± 0.044, 0.532 ± 0.031 mm for groups 1, 2 and 3, respectively; p = 0.89). However, there was a significant tendency toward corneal thinning with a longer history of contact lens wear (r = –0.31, p = 0.002 in groups 2 and 3). The percentage of hexagonal cells decreased with both increasing hours of contact lens wear per day (r = –0.36, p < 0.001) and the duration of contact lens wear in years (r = –0.33, p < 0.001), but there was no significant change in endothelial cell density in contact lens wearers. The coefficient of variation in cell size correlated more closely with increased hours of contact lens wear per day (r = 0.35, p = 0.002) than with the duration of contact lens wear in years (r = 0.12; p = 0.31). In the functional study, corneal autofluorescence increased in contact lens wearers (5.13 ± 0.71 ng/ml in group 1, 6.45 ± 2.03 ng/ml in group 2 and 7.21 ± 1.51 ng/ml in group 3, respectively, p < 0.001) and the mean endothelial permeability decreased in contact lens wearers (3.89 ± 0.95 ×10–4/cm in group 1, 2.71 ± 0.73 × 10–4/cm in group 2 and 2.95 ± 0.91 × 10–4/cm in group 3, respectively, p = 0.003). Conclusions: Daily wear soft contact lenses caused morphological changes in the corneal endothelium. With an increasing span of contact lens wear, there was a significantly increased variation in cell size, a decreased hexagonal cell percentage, an evident intercellular dark area and rosette formation. The corneal autofluorescence increased and the overall endothelial permeability decreased as a consequence of contact lens wear. Contact lens wear also caused corneal thinning, and the cornea became thinner with increasing duration of contact lens wear.