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Objective This study aimed to explore patient experience and preferences for different investigation modalities for surveillance and assessment of disease activity and mucosal healing in patients with established Crohn’s disease (CD).Method A qualitative interview study embedded within a UK-based pragmatic trial of panenteric capsule endoscopy (PillCam™ Crohn’s capsule, PCC) compared with ileocolonoscopy (IC) and magnetic resonance enterography (MRE). Telephone semi-structured interviews were completed with 10 patients with established CD who had undergone all three modalities.Results A range of advantages and disadvantages relating to all three modalities were described. PCC was generally reported as being easy to swallow and associated with less discomfort, intrusiveness and pain than IC. Negative attributions associated with unpleasantness of IC were common; however, the intensity of associated emotions, rather than their presence, seems to have the greatest influence on procedure preference. Tolerance of investigative procedures can be moderated by acceptance and recognition of their necessity in management of CD and perceived effectiveness of the procedures. Other key influences include the importance of support and trust in clinical and nursing staff and the ability to manage procedure and appointment requirements within daily life and responsibilities.Conclusions Findings suggest that for many, although not all, patients with CD, there would be a clear preference for PCC over IC and MRE, if effectiveness is proven to be equivalent. This supports the need for further work to demonstrate use and effectiveness with a view to integration within current management guidelines and care pathways in line with patient preference.Trial registration number NCT04274010.