Objective. To compare macular thickness (MT) and retinal nerve fiber layers (RNFL) between women with polycystic ovary syndrome (PCOS) and healthy women. Materials and Methods. The study included 45 women with PCOS and 47 ovulatory women undergoing clinical-gynecological and ophthalmic evaluations, including measurement of MT, RNFL, and optic disc parameters using optical coherence tomography. Results. The superior RNFL around the optic nerve was significantly thicker in PCOS than in healthy volunteers (P = 0.036). After stratification according to insulin resistance, the temporal inner macula (TIM), the inferior inner macula (IIM), the nasal inner macula (NIM), and the nasal outer macula (NOM) were significantly thicker in PCOS group than in control group (P < 0.05). Both the presence of obesity associated with insulin resistance (P = 0.037) and glucose intolerance (P = 0.001) were associated with significant increase in the PC1 mean score, relative to MT. A significant increase in the PC2 mean score occurred when considering the presence of metabolic syndrome (P < 0.0001). There was a significant interaction between obesity and inflammation in a decreasing mean PC2 score relative to macular RNFL thickness (P = 0.034). Conclusion. Decreased macular RNFL thickness and increased total MT are associated with metabolic abnormalities, while increased RNFL thickness around the optic nerve is associated with hormonal changes inherent in PCOS.