To identify any structural differences in macular choroidal thickness in migraine patients and compare them with that of control subjects by using spectral domain optic coherence tomography (SD-OCT). In this prospective study, choroidal thicknesses of 32 migraine patients during migraine attack-free period and 32 age-and sex-matched healthy subjects were measured using SD-OCT. All patients underwent a complete ophthalmic examination before the measurements. The migraine patients were classified into the migraine with aura group or the migraine without aura group. Migraine severity was assessed by visual analog scale (VAS), migraine disability questionnaire (Migraine Disability Assessment Score (MIDAS), and Wong-Baker faces pain rating scale. Thirty eyes of 32 subjects (31 female and 1 male) in the migraine group and 32 eyes of 32 subjects (31 female and 1 male) in control group were evaluated. In the study group, 16 patients suffered migraine without aura (MWA) and 16 patients were diagnosed as migraine with aura (MA). The mean subfoveal choroidal thickness (SFCT) was 353.3 +/- 66.5 mu m in the control group versus 304.3 +/- 72.9 mu m and 276.1 +/- 61.4 mu m in MWA and MA groups, respectively. The difference in SFCT between the migraine patients and the controls was significant (p < 0.001). Additionally, a moderate correlation was found between SFCT and the VAS score and W baker score (r = 0.48, p = 0.008 and r = 0.43, p = 0.02, respectively). The choroidal thickness was found to decrease significantly not only in migraine patients with aura but also in those without aura during the attack-free period.