Purpose To evaluate the effects of Fabry disease (FD) on the retinal microvasculature and choroidal vascular and structural characteristics. Methods This study included 10 patients with FD and 10 age-matched healthy controls. Binarized enhanced depth imaging optical coherence tomography (OCT) images were used to measure the total choroidal area, luminal area, and stromal area with ImageJ software. The choroidal vascularity index (CVI) was assessed. The vessel densities (VD) of the retinal capillary plexuses and foveal avascular zone (FAZ) area were measured with OCT-angiography. Results The most common anterior segment finding was cornea verticillata (60.0%) and the most frequent posterior segment finding was vascular tortuosity (50.0%). Intraretinal hyperreflective foci on B-scan OCT was observed in 50.0% of the cases. In Fabry cases, a linear mixed model with random intercept revealed that 1% change in CVI was related to -0.009 mm(2) (p = .015) change in FAZ area and -0.047 mm change, (p = .024) in FAZ perimeter. In the presence of retinal vascular tortuosity, 1% change in CVI was related to -0.013 mm(2) (p = .002) change in FAZ area and -0.052 mm change (p = .004) in FAZ perimeter. In the presence of hyperreflective foci, 1% change in CVI was related to -0.014 mm(2) (p = .004) change in FAZ area and -0.064 mm change (p = .003) in FAZ perimeter. Conclusion The significant negative associations between FAZ measurements and CVI suggest a possible interaction between the choroidal and retinal microvasculature of patients with FD. These alterations were more pronounced in the presence of hyperreflective foci and retinal vascular tortuosity.