ABSTRACT: OBJECTIVES:To compare patient acceptability and burden of magnetic resonance enterography (MRE) and ultrasound (US) to each other, and to other enteric investigations, particularly colonoscopy. METHODS:159 patients (mean age 38, 94 female) with newly diagnosed or relapsing Crohn's disease, prospectively recruited to a multicentre diagnostic accuracy study comparing MRE and US completed an experience questionnaire on the burden and acceptability of small bowel investigations between December 2013 and September 2016. Acceptability, recovery time, scan burden and willingness to repeat the test were analysed using the Wilcoxon signed rank and McNemar tests; and group differences in scan burden with Mann-Whitney U and Kruskal-Wallis tests. RESULTS:Overall, 128 (88%) patients rated MRE as very or fairly acceptable, lower than US (144, 99%; p < 0.001), but greater than colonoscopy (60, 60%; p < 0.001). MRE recovery time was longer than US (p < 0.001), but shorter than colonoscopy (p < 0.001). Patients were less willing to undergo MRE again than US (127 vs. 133, 91% vs. 99%; p = 0.012), but more willing than for colonoscopy (68, 75%; p = 0.017). MRE generated greater burden than US (p < 0.001), although burden scores were low. Younger age and emotional distress were associated with greater MRE and US burden. Higher MRE discomfort was associated with patient preference for US (p = 0.053). Patients rated test accuracy as more important than scan discomfort. CONCLUSIONS:MRE and US are well tolerated. Although MRE generates greater burden, longer recovery and is less preferred than US, it is more acceptable than colonoscopy. Patients, however, place greater emphasis on diagnostic accuracy than burden. KEY POINTS:• MRE and US are rated as acceptable by most patients and superior to colonoscopy. • MRE generates significantly greater burden and longer recovery times than US, particularly in younger patients and those with high levels of emotional distress. • Most patients prefer the experience of undergoing US than MRE; however, patients rate test accuracy as more importance than scan burden.