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Background: Guidelines suggest computed tomography colonography (CTC) following incomplete optical colonoscopy (OC). Colon capsule endoscopies (CCE) have been suggested as an alternative, although completion rates have been unsatisfactory. Introduction of artificial intelligence (AI)-based localization algorithms of the camera capsules may enable identification of incomplete CCE investigations overlapping with incomplete OCs., Objective: The study aims to investigate relative sensitivity of CCE compared with CTC following incomplete OC, investigate the completion rate when combining results from the incomplete OC and CCE, and develop a forward-tracking algorithm ensuring a safe completeness of combined investigations., Methods: In this prospective paired study, patients with indication for CTC following incomplete OC were included for CCE and CTC. Location of CCE abortion and OC abortion were registered to identify complete combined investigations. AI-based algorithm for localization of capsules were developed reconstructing the passage of the colon., Results: In 237 individuals with CTC indication; 105 were included, of which 97 underwent both a CCE and CTC. CCE was complete in 66 (68%). Including CCEs which reached most oral point of incomplete OC, 73 (75%) had complete colonic investigations; 78 (80%) had conclusive investigations. Relative sensitivity of CCE compared with CTC was 2.67 (95% confidence interval (CI) 1.76;4.04) for polyps >5 mm and 1.91 (95% CI 1.18;3.09) for polyps >9 mm. An AI-based algorithm was developed., Conclusion: Sensitivity of CCE following incomplete OC was superior to CTC. Introducing and improving algorithm-based localization of capsule abortion may increase identification of overall complete investigation rates following incomplete OC.ClinicalTrials.gov identifier: NCT02826993.