Purpose: To investigate the retinal and choroidal microcirculation changes in celiac disease (CD) patients via optical coherence tomography angiography (OCT-A). Methods: This cross-sectional study included 44 pediatric patients with newly diagnosed CD and 44 healthy pediatric subjects. The vascular densities (VD) of the superficial, deep, and choriocapillar plexuses (VDs, VDd, and VDcc, respectively) (%), the superficial and deep foveal avascular zones (FAZs and FAZd) (%), the central macular thickness (CMT) (μm), and the subfoveal choroidal thickness (SFCT) (μm) were measured with swept-source OCT-A in addition to a complete ophthalmological examination. Results: Mean ages of the CD patients and the healthy participants were 12.02 ± 2.9 and 13.6 ± 2.3 years, respectively. The central sectors of the VDs and VDd measurements were found to be significantly higher in the study group compared to the control group (p = 0.006; P = 0.001, respectively), and the temporal and nasal values of the VDcc measurements were significantly lower in the study group than in the control group (p < 0.05 for both values). CMT and FAZ metrics did not differ between the groups (p > 0.05). SFCT was significantly reduced (p = 0.001), and choroidal thinning was more considerable in female CD patients (p = 0.045). Conclusion: CD seems to affect macular and choroidal microcirculation. The reduced choriocapillaris plexus parameters and choroidal thickness may provide disease activity information.