Purpose To measure the effects of long-term wear of soft lenses of low and high oxygen transmissibility (Dk) on basal epithelial appearance and epithelial thickness. Methods Sixty-three subjects were enroled in a cross-sectional study. Seventeen high Dk lens wearers and 24 low Dk lens wearers who had worn lenses on an extended wear basis for more than 3 years (range: 3-22) were compared to a group of 22 age-matched subjects who had never worn contact lenses. Cell regularity and the intensity of light backscattered by the basal epithelium were assessed using confocal microscopy. Epithelial thickness was measured at the centre and at four peripheral locations using modified optical pachometry. Results Epithelial basal cells appeared less regular in low Dk lens wearers than high Dk wearers or controls (Mann-Whitney U-test, P ¼ 0.001). The intensity of backscattered light did not differ across groups (Kruskal-Wallis test, P ¼ 0.37). Low Dk wearers had the thinnest epithelium (46 (10) mm), followed by high Dk wearers (54 (14) mm) and controls (58 (9) mm; ANOVA, Pp0.006). Topographical position did not affect epithelial thickness (ANOVA, P ¼ 0.10). Conclusions Visible alterations to the basal epithelial cells can only be detected in longterm extended wearers of low Dk soft lenses. Extended wear of high Dk soft lenses results in topographically uniform epithelial thinning that is significantly less than the thinning seen with low Dk lenses. Confirmation of these findings using groups with evenly matched duration of lens wear is required.