Following incomplete colonoscopy (IC) patients often undergo computed tomography colonography (CTC), but colon capsule endoscopy (CCE) may be an alternative. We compared the completion rate, sensitivity and diagnostic yield for polyp detection from CCE and CTC following IC. A systematic literature search resulted in twenty-six studies. Extracted data included inter alia, complete/incomplete investigations and polyp findings. Pooled estimates of completion rates of CCE and CTC and complete colonic view rates (CCE reaching the most proximal point of IC) of CCE were calculated. Per patient diagnostic yields of CCE and CTC were calculated stratified by polyp sizes. CCE completion rate and complete colonic view rate were 76% (CI 95% 68–84%) and 90% (CI 95% 83–95%). CTC completion rate was 98% (CI 95% 96–100%). Diagnostic yields of CTC and CCE were 10% (CI 95% 7–15%) and 37% (CI 95% 30–43%) for any size, 13% (CI 95% 9–18%) and 21% (CI 95% 12–32%) for >5-mm and 4% (CI 95% 2–7%) and 9% (CI 95% 3–17%) for >9-mm polyps. No study performed a reference standard follow-up after CCE/CTC in individuals without findings, rendering sensitivity calculations unfeasible. The increased diagnostic yield of CCE could outweigh its slightly lower complete colonic view rate compared to the superior CTC completion rate. Hence, CCE following IC appears feasible for an introduction to clinical practice. Therefore, randomized studies investigating CCE and/or CTC following incomplete colonoscopy with a golden standard reference for the entire population enabling estimates for sensitivity and specificity are needed.