Background: To compare the optical density of iris pigment epithelium (ODIPE) and iris stromal thickness (IST) measurements in patients having pseudoexfoliation syndrome (PXS) and age-gender matched participants. Methods: This is a cross-sectional study. Patients with PXS were enrolled in the study group. Age and gendermatched healthy subjects with no evidence of PXS were recruited as controls. After a comprehensive ophthalmological evaluation, the anterior segment images were acquired using anterior segment spectral-domain optical coherence tomography (AS SD-OCT). The acquired pictures were further analyzed using the ImageJ program. Two investigators measured the ODIPE and the IST of the subjects, and the repeatability and reproducibility were checked. SPSS program was used for statistical analysis. Results: The PXS group was comprised of twenty-two eyes (n = 22 patients), and the control group contained twenty-six eyes of 26 age and gender-matched healthy subjects. The mean temporal ODIPE of the study group was found to be decreased significantly in comparison to the mean temporal ODIPE of the control eye (p = 0.018). Both the mean nasal (N) and temporal (T) ISTs of the PEX eyes were thinner than the control eyes (p = 0.006 and p = 0.002, respectively). The mean baseline IOP was found to significantly negatively correlate with the ODIPE in the PEX group at both N and T sides (r = -0.531, p = 0.011 and r = -0.685, p < 0.001, respectively). Conclusion: The pupillary margin IPE was found more depigmented, and the mean N and T IST were significantly thinner in the PEX group by comparison with the age-gender matched healthy controls. The mean baseline IOP was negatively correlated with the pupillary margin's IPE pigmentation degree in patients with PXS.