© 2021 Taylor & Francis Group, LLC.Purpose of the study: To investigate the change in individual retinal layer thickness by spectral-domain optical coherence tomography (SD-OCT) in eyes underwent femtosecond laser-assisted laser in situ keratomileusis (FS-LASIK) and photorefractive keratectomy (PRK). Methods: In patients who underwent PRK and FS-LASIK, changes in the thickness of all retinal layers in the foveal, parafoveal, and perifoveal regions were evaluated by SD-OCT automated segmentation analysis at pre-operatively and different time points post-operatively. Results: Seventy-one eyes of 71 patients (38 patients in PRK, 33 patients in LASIK) were included. In the pre-operative period, mean spherical equivalent (SE), mean keratometry, axial length, and segmentation values of the retinal layers were similar (P> .05). In the PRK group, the pre-operative measurements of individual retinal layers did not show a statistically significant difference compared to the post-operative measurements on the 1st day, 1st week, and 1st month. In the FS-LASIK group, the mean inner nuclear layer (INL) thickness one day after the surgery was significantly higher than that before surgery in the foveal (21.22 ± 4.66 µm vs 19.03 ± 4.50 µm, P= .013) and parafoveal regions (41.98 ± 3.70 µm vs 40.56 ± 3.49 µm, P= .044). Conclusions: The findings of our study suggest that the increase of INL thickness may be due to temporary structural and circulatory changes of the retina that may occur in the suction phase in the FS-LASIK procedure.