This observational case–control study assessed the differences in choroidal structure between patients with celiac disease and healthy subjects utilizing the choroidal vascularity index (CVI). Seventy-four celiac patients and 67 healthy subjects underwent a complete ophthalmological evaluation, axial length (AL) measurements and spectral-domain optical coherence tomography with enhanced depth imaging mode (EDI SD-OCT) evaluation. These images were binarized and choroidal vasculature was analyzed. Choroidal total subfoveal area (TSA), luminal subfoveal area (LSA), stromal subfoveal area (SSA), CVI and subfoveal choroidal thickness (CT) were measured. Furthermore, subfoveal CT, TSA, LSA, SSA, and CVI were also correlated with AL. A statistically significant difference was found between the two groups for TSA, LSA, SSA and subfoveal CT, but not for CVI. In celiac patients, a significant correlation was found between AL and TSA, LSA and SSA, but not with CVI. Similar findings were also noticed in the healthy subjects. Thus, celiac patients have a thicker choroid than healthy subjects, regardless of the AL, due to a proportional increase in both the vascular and stromal components, which does not alter the CVI.