Introduction: Nasal septal deviation (NSD) is one of the major causes of upper airway obstruction. Chronic hypoxia and hypercapnia due to NSD may affect the choroidal blood flow and may change the choroidal thickness (CT). In this study, the authors aimed to research the assessment of CT before and after septoplasty in patients with NSD. Methods: Ninety-two patients who underwent septoplasty surgery with the diagnose of nasal septum deviation and 58 patients for control group were enrolled to the study. CT values measured before and three months after septoplasty surgery. Results: CT values were subfoveal 272.51 +/- 27.62, nasal 245.50 +/- 21.22, temporal 248.35 +/- 30.25 and subfoveal 232.09 +/- 44.17, nasal 222.09 +/- 38.82,temporal 227.12 +/- 28.80 for the control and NSD groups, respectively (P < 0.001). Also choroid thickness values (subfoveal 232.09 +/- 44.17, nasal 222.09 +/- 38.82, temporal 227.12 +/- 28.80; subfoveal 252 +/- 18.90, nasal 228 +/- 22.12, temporal 240 +/- 25.80) were significantly different in patients with NSD, before and after septoplasty procedure, respectively (P < 0.001). Conclusion: To the authors' knowledge this is the first study investigating choroid thickness measurements before and after septoplasty in patients with NSD. We found significant correlation between NSD and CT. After septoplasty surgery at 3rd month, CT increased significantly in comparision with the preoperative values.