Background: Endoscopy and biopsy are used to diagnose coeliac disease. There are, however, observerdependent interpretations of the degree of villous atrophy in biopsies. A pilot study using quantitative imageprocessing procedures was performed to quantify the degree of villous atrophy in patients with coeliac disease. Method: The degree of villous atrophy in duodenal biopsy images was quantified by calculating the ratio of villous edge-to-piecewise arc length (E/P ratio), and this value was compared with the blinded assessment of Marsh score for degree of villous atrophy. Results: Mean E/P ratios for n = 31 biopsy images, 2.76 (SD 0.44) (Marsh Illa), 1.91 (0.50) (Marsh Illb) and 1.18 (0.22) (Marsh Illc), were significantly different (p = 0.006). Based on non-parametric testing, the E/P ratios were inversely correlated with Marsh scores (Spearman coefficient p = -0.798, Kendall τ = -0.681; p<0.0001). Conclusions: Biopsy images quantified by image analysis correlated exceedingly well with the histopathological grade of villous atrophy. Since quantified measurements are real-numbered values and lack observer bias, measurement of villous atrophy based on image analysis lends itself to standardisation of histological grading.