Objectives To evaluate the ocular surface, meibomian glands and corneal structural changes using in vivo confocal microscopy (IVCM) in patients receiving aromatase inhibitor (AI) therapy due to the breast cancer. Methods This prospective observational study included 13 patients undergoing AI therapy. The patients were evaluated before the treatment, at 3- and 6-month timepoints of AI therapy. To examine the ocular surface and tear film, corneal sensitivity (CS) measurement with Cochet-Bonnet Aesthesiometer, tear film break-up time (TBUT), lissamine green (LG) staining, Schirmer I test with anaesthesia (ST) and the ocular-surface disease index (OSDI) questionnaire were performed consecutively. Corneal cell densities and sub-basal nerve plexus were evaluated with IVCM (ConfoScan 4, Nidek, Japan). Finally, quantitative MG drop-out assessment was made using infrared meibography. Shapiro Wilk, Friedman's and Post-hoc Dunn tests were used for the statistical analysis. Results TBUT, ST scores, basal epithelium, anterior and posterior keratocytes and endothelial cell densities, long and total sub-basal nerve densities were found to be decreased (p < 0.001, p = 0.023, p < 0.001, p = 0.01, p = 0.002, p = 0.004, p < 0.001, p < 0.001), and meiboscore, CS, OSDI scores and sub-basal nerve tortuosity values were increased (p < 0.001, p = 0.015, p = 0.001, p = 0.004) during the treatment. Endothelial pleomorphism rates were lower at the 3- and 6-month timepoints compared to before the treatment (p = 0.04). Conclusion This study showed that aromatase inhibitor therapy causes deteriorations in many of the ocular-surface parameters and corneal structural changes in relation with the duration of treatment. These patients should be observed during the therapy in terms of the ocular-surface side effects.