Background and AimsSmall bowel capsule endoscopy (SBCE) has an established role in patients with non-responsive celiac disease (CeD). A non-invasive method to quantify small bowel atrophy is still lacking. MethodsWe analysed SBCE frames from CeD patients from 2018 to 2020. Histology was the reference standard, with atrophy defined as Marsh-Oberhuber score ≥ 3a. Three regions of interest (ROI) were blindly selected from each frame by an expert gastroenterologist and analysed using a National Institute of Health J image-processing software into a numerical scale. A 3D surface plot macro identified intestinal villi density through isolines plots. ResultsWe acquired 306 ROIs from 57 frames with macroscopic atrophy and 45 with normal mucosa. Frames were classified as atrophic (n = 63) or non-atrophic (n = 39) per Marsh-Oberhuber classification. Median density score significantly differed between atrophic and non-atrophic frames (p < 0.001). The morphometric analysis showed a sensitivity of 77 % and a specificity of 79 % in discriminating between atrophic or non-atrophic mucosa with a 14.10 cut-off (Youden Index) and an overall AUC of 0.805 (CI 95 % 0.712–0.897). ConclusionsOur newly developed SBCE software can effectively quantify villous atrophy. Further studies are needed to validate its applicability in an external cohort.