Objective: To compare the choroidal thickness in pseudoexfoliation syndrome (PES) and pseudoexfoliative glaucoma (PEG) cases with healthy individuals. Material and Methods: We included 31 eyes of 31 patients with PES, 31 eyes of 31 patients with PEG, and 33 eyes of 33 healthy individuals in this study. All patients underwent choroidal thickness measurement at the subfoveal, nasal 500 µm, nasal 1000 µm, temporal 500 µm, and temporal 1000 µm areas by using the optical coherence tomography (3D OCT-2000, Topcon, Japan) device. Results: There was no difference between the groups for gender and axial length (p>0.05). The subfoveal, nasal 500 µm and temporal 500 µm choroidal thickness values of the PEG cases were statistically significantly lower than the PES cases and the healthy group (p0.05). Conclusion: We found the subfoveal, nasal 500 µm and temporal 500 µm choroidal thicknesses to be significantly lower in the PEG cases than the other two groups. Choroidal thicknesses at the subfoveal and nasal 500 µm areas were also lower in the PES group than the control group but without statistical significance.