OBJECTIVE: To investigate patient experience of CT colonography (CTC) and colonoscopy in a national screening programme. METHODS: Retrospective analysis of patient experience postal questionnaires. We included screenees from a fecal occult blood test (FOBt) based screening programme, where CTC was performed when colonoscopy was incomplete or deemed unsuitable. We analyzed questionnaire responses concerning communication of test risks, test-related discomfort and post-test pain, as well as complications. CTC and colonoscopy responses were compared using multilevel logistic regression. RESULTS: Of 67,114 subjects identified, 52,805 (79 %) responded. Understanding of test risks was lower for CTC (1712/1970 = 86.9 %) than colonoscopy (48783/50975 = 95.7 %, p < 0.0001). Overall, a slightly greater proportion of screenees found CTC unexpectedly uncomfortable (506/1970 = 25.7 %) than colonoscopy (10,705/50,975 = 21.0 %, p < 0.0001). CTC was tolerated well as a completion procedure for failed colonoscopy (unexpected discomfort; CTC = 26.3 %: colonoscopy = 57.0 %, p < 0.001). Post-procedural pain was equally common (CTC: 288/1970,14.6 %, colonoscopy: 7544/50,975,14.8 %; p = 0.55). Adverse event rates were similar in both groups (CTC: 20/2947 = 1.2 %; colonoscopy: 683/64,312 = 1.1 %), but generally less serious with CTC. CONCLUSIONS: Even though CTC was reserved for individuals either unsuitable for or unable to complete colonoscopy, we found only small differences in test-related discomfort. CTC was well tolerated as a completion procedure and was extremely safe. CTC can be delivered across a national screening programme with high patient satisfaction. KEY POINTS: • High patient satisfaction at CTC is deliverable across a national screening programme. • Patients who cannot tolerate screening colonoscopy are likely to find CTC acceptable. • CTC is extremely safe; complications are rare and almost never serious. • Patients may require more detailed information regarding the expected discomfort of CTC.