OBJECTIVES: To assess whether electronic cleansing (EC) of tagged residue and different computed tomography (CT) windows influence the size of colorectal polyps in CT colonography (CTC). METHODS: A database of 894 colonoscopy-validated CTC datasets of a low-prevalence cohort was retrospectively reviewed to identify patients with polyps ≥6 mm that were entirely submerged in tagged residue. Ten radiologists independently measured the largest diameter of each polyp, two-dimensionally, before and after EC in colon, bone, and soft-tissue-windows, in randomised order. Differences in size and polyp count before and after EC were calculated for size categories ≥6 mm and ≥10 mm. Statistical testing involved 95% confidence interval, intraclass correlation and mixed-model ANOVA. RESULTS: Thirty-seven patients with 48 polyps were included. Mean polyp size before EC was 9.8 mm in colon, 9.9 mm in bone and 8.2 mm in soft-tissue windows. After EC, the mean polyp size decreased significantly to 9.4 mm in colon, 9.1 mm in bone and 7.1 mm in soft-tissue windows. Compared to unsubtracted colon windows, EC, performed in colon, bone and soft-tissue windows, led to a shift of 6 (12,5%), 10 (20.8%) and 25 (52.1%) polyps ≥6 mm into the next smaller size category, thus affecting patient risk stratification. CONCLUSIONS: EC and narrow CT windows significantly reduce the size of polyps submerged in tagged residue. Polyp measurements should be performed in unsubtracted colon windows. KEY POINTS: • EC significantly reduces the size of polyps submerged in tagged residue. • Abdominal CT-window settings significantly underestimate 2D sizes of submerged polyps. • Size reduction in EC is significantly greater in narrow than wide windows. • Underestimation of polyp size due to EC may lead to inadequate treatment. • Polyp measurements should be performed in unsubtracted images using a colon window.