Background <p>This study aimed to evaluate structural and microvascular changes in amblyopic eyes using optical coherence tomography (OCT) and optical coherence tomography angiography (OCTA), and to compare these findings with those of fellow eyes and healthy individuals.</p> Methods <p>This is a cross-sectional controlled study. Retinal and choroidal structures were examined using the Spectralis OCT device (Spectralis, Heidelberg Engineering, Heidelberg, Germany), and vascular analyses were performed with the Topcon Triton SS-OCT (Topcon Triton, Tokyo, Japan). Structural parameters such as macular thickness, ganglion cell layer (GCL), inner plexiform layer (IPL), peripapillary retinal nerve fiber layer (PpRNFL), and choroidal thickness were measured. Additionally, luminal area (LA), total choroidal area (TCA), and choroidal vascular index (CVI) were calculated. Group comparisons were performed using linear mixed-effects models to account for the non-independence of amblyopic and fellow eyes.</p> Results <p>A total of 130 individuals were included in the study: 65 patients and 65 control subjects. The study included 65 amblyopic eyes (Group 1), 65 clinically healthy fellow eyes from the same patients (Group 2), and 65 healthy control eyes (Group 3). Amblyopic eyes were further divided into two groups: those with amblyopia due to anisometropia (Group 1&#xa0;A) and those with amblyopia due to strabismus (Group 1B). Choroidal thickness was higher in Groups 1 and 2 compared to Group 3. OCTA values were not significantly different between the groups. Macular thickness, except for foveal macular thickness, was thicker in Groups 1 and 2 compared to Group 3. Foveal macular thickness was not significantly different between the groups. Several significant sectoral differences in GCL measurements were observed among the groups. The inner and outer sectors of the inner plexiform layer were significantly thicker in Groups 1 and 2 compared to Group 3, whereas foveal IPL thickness did not differ significantly among the main groups. In PpRNFL measurements, the temporal superior quadrant was thinner in both the amblyopic and fellow eye groups compared to the control group, whereas the nasal inferior quadrant was thicker in the amblyopic eye group than in the fellow eye and control groups. There were no differences between the groups in PpRNFL in the other quadrants. In CVI measurements, the control group had higher CVI values compared to both the amblyopic and healthy eyes.</p> Conclusions <p>Amblyopia was associated with structural retinal and choroidal differences, whereas OCTA parameters did not differ significantly among the groups. Future larger-scale and longitudinal studies may better elucidate the contribution of retinal microvascular changes to the pathophysiology of amblyopia.</p>