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Purpose: To investigate the effect of oral isotretinoin therapy on central macular thickness (CMT) thickness and choroidal thickness (CT) using optical coherence tomography (OCT)., Methods: CT and CMT thickness of 43 eyes were evaluated at baseline, the third, and sixth month of isotretinoin therapy by spectral-domain OCT. For assessment of CT, OCT measurements were obtained at the fovea with six additional measurements at adjacent locations (at 500-1000 µm temporal to the fovea and 500-1000 µm nasal to the fovea)., Results: Forty-three eyes from 43 patients with acne vulgaris, including 33 females (76.7%), who had a mean age of 24.81 ± 6.60 years, completed the study. The mean CMT was 231.49 ± 19.52 at the baseline and significantly decreased to 229.0 ± 19.57 ( p  = 0.02) and 229.28 ± 18.83 after three and six months, respectively ( p  < 0.03). The change in the macular thicknesses measured at four quadrants and choroidal thicknesses were not statistically significant during the study ( p  > 0.05)., Conclusion: The result of our study demonstrated choroidal thickness change is not significant in patients with acne vulgaris after systemic isotretinoin therapy during six months of follow-up. The decreased CMT amount was 2.2 microns; even if statistically significant, this amount is clinically insignificant.