Background: Magnetic resonance enterography and enteric ultrasonography are used to image Crohn's disease patients. Their diagnostic accuracy for presence, extent and activity of enteric Crohn's disease was compared., Objective: To compare diagnostic accuracy, observer variability, acceptability, diagnostic impact and cost-effectiveness of magnetic resonance enterography and ultrasonography in newly diagnosed or relapsing Crohn's disease., Design: Prospective multicentre cohort study., Setting: Eight NHS hospitals., Participants: Consecutive participants aged ≥ 16 years, newly diagnosed with Crohn's disease or with established Crohn's disease and suspected relapse., Interventions: Magnetic resonance enterography and ultrasonography., Main Outcome Measures: The primary outcome was per-participant sensitivity difference between magnetic resonance enterography and ultrasonography for small bowel Crohn's disease extent. Secondary outcomes included sensitivity and specificity for small bowel Crohn's disease and colonic Crohn's disease extent, and sensitivity and specificity for small bowel Crohn's disease and colonic Crohn's disease presence; identification of active disease; interobserver variation; participant acceptability; diagnostic impact; and cost-effectiveness., Results: Out of the 518 participants assessed, 335 entered the trial, with 51 excluded, giving a final cohort of 284 (133 and 151 in new diagnosis and suspected relapse cohorts, respectively). Across the whole cohort, for small bowel Crohn's disease extent, magnetic resonance enterography sensitivity [80%, 95% confidence interval (CI) 72% to 86%] was significantly greater than ultrasonography sensitivity (70%, 95% CI 62% to 78%), with a 10% difference (95% CI 1% to 18%; p = 0.027). For small bowel Crohn's disease extent, magnetic resonance enterography specificity (95%, 95% CI 85% to 98%) was significantly greater than ultrasonography specificity (81%, 95% CI 64% to 91%), with a 14% difference (95% CI 1% to 27%). For small bowel Crohn's disease presence, magnetic resonance enterography sensitivity (97%, 95% CI 91% to 99%) was significantly greater than ultrasonography sensitivity (92%, 95% CI 84% to 96%), with a 5% difference (95% CI 1% to 9%). For small bowel Crohn's disease presence, magnetic resonance enterography specificity was 96% (95% CI 86% to 99%) and ultrasonography specificity was 84% (95% CI 65% to 94%), with a 12% difference (95% CI 0% to 25%). Test sensitivities for small bowel Crohn's disease presence and extent were similar in the two cohorts. For colonic Crohn's disease presence in newly diagnosed participants, ultrasonography sensitivity (67%, 95% CI 49% to 81%) was significantly greater than magnetic resonance enterography sensitivity (47%, 95% CI 31% to 64%), with a 20% difference (95% CI 1% to 39%). For active small bowel Crohn's disease, magnetic resonance enterography sensitivity (96%, 95% CI 92% to 99%) was significantly greater than ultrasonography sensitivity (90%, 95% CI 82% to 95%), with a 6% difference (95% CI 2% to 11%). There was some disagreement between readers for both tests. A total of 88% of participants rated magnetic resonance enterography as very or fairly acceptable, which is significantly lower than the percentage (99%) of participants who did so for ultrasonography. Therapeutic decisions based on magnetic resonance enterography alone and ultrasonography alone agreed with the final decision in 122 out of 158 (77%) cases and 124 out of 158 (78%) cases, respectively. There were no differences in costs or quality-adjusted life-years between tests., Limitations: Magnetic resonance enterography and ultrasonography scans were interpreted by practitioners blinded to clinical data (but not participant cohort), which does not reflect use in clinical practice., Conclusions: Magnetic resonance enterography has higher accuracy for detecting the presence, extent and activity of small bowel Crohn's disease than ultrasonography does. Both tests have variable interobserver agreement and are broadly acceptable to participants, although ultrasonography produces less participant burden. Diagnostic impact and cost-effectiveness are similar. Recommendations for future work include investigation of the comparative utility of magnetic resonance enterography and ultrasonography for treatment response assessment and investigation of non-specific abdominal symptoms to confirm or refute Crohn's disease., Trial Registration: Current Controlled Trials ISRCTN03982913., Funding: This project was funded by the National Institute for Health Research (NIHR) Health Technology Assessment programme and will be published in full in Health Technology Assessment ; Vol. 23, No. 42. See the NIHR Journals Library website for further project information., Competing Interests: Stuart A Taylor reports personal fees from Robarts Clinical Trials Inc. (London, ON, Canada) outside the submitted work. Simon Travis reports receiving fees for consultancy work and/or speaking engagements from the following: AbbVie Inc. (Chicago, IL, USA), Centocor Inc. (Horsham, PA, USA), Schering-Plough (Kenilworth, NJ, USA), Bristol-Myers Squibb (New York, NY, USA), Chemocentryx Inc. (Mountain View, CA, USA), Cosmo Pharmaceuticals (Dublin, Ireland), Elan Pharma Inc. (Dublin, Ireland), Genentech Inc. (San Francisco, CA, USA), Giuliani SpA (Milan, Italy), Merck & Co. Inc. (Kenilworth, NJ, USA), Takeda UK Ltd (Woodburn Green, Buckinghamshire, UK), Otsuka Pharmaceuticals (Tokyo, Japan), PDL BioPharma (Nevada, NV, USA), Pfizer Inc. (San Francisco, CA, USA), Shire Pharmaceuticals UK (St Helier, Jersey), Glenmark Pharmaceuticals (Maharashtra, India), Synthon Biopharmaceuticals (Nijmegen, the Netherlands), NPS Pharmaceuticals (Bedminster, NJ, USA), Eli Lilly and Company (Indiana, IN, USA), Warner Chilcott Ltd, Proximagen Group Ltd (London, UK), VHsquared Ltd (Cambridge, UK), Topivert Pharma Ltd (London, UK), Ferring Pharmaceuticals (Saint-Prex, Switzerland), Celgene Corporation (Summit, NJ, USA), GlaxoSmithKline plc (Brentford, UK), Amgen Inc. (Thousand Oaks, CA, USA), Biogen Inc. (Cambridge, MA, USA), Enterome SA (Paris, France), Immunocore Ltd (Oxford, UK), Immunometabolism/Third Rock Ventures (Boston, MA, USA), Bioclinica Inc. (Newtown, PA, USA), Boehringer Ingelheim GmBH (Ingelheim am Rhein, Germany), Gilead Sciences Inc. (Foster City, CA, USA), Grunenthal Ltd (Aachen, Germany), Janssen Pharmaceutica (Beerse, Belgium), Novartis AG (Basel, Switzerland), Receptos Inc. (San Diego, CA, USA), Pharm-Olam International UK Ltd (Bracknell, UK), Sigmoid Pharma (Dublin, Ireland), Theravance Biopharma Inc. (Dublin, Ireland), Given Imaging Ltd (Yokneam Illit, Israel), UCB Pharma SA (Brussels, Belgium), Tillotts Pharma AG (Rheinfelden, Switzerland), Sanofi Aventis SA (Paris, France), Vifor Pharma (St Gallen, Switzerland), Abbott Laboratories Ltd (Chicago, IL, USA) and Procter and Gamble Ltd (Cincinnati, OH, USA). Simon Travis reports directorships of charities IBD2020 (Barnet, UK; UK 09762150), Cure Crohn’s Colitis (Sydney, Australia; ABN 85 154 588 717) and the Truelove Foundation (London, UK; UK 11056711). Simon Travis also reports receiving fees from the following for expert testimony work and/or royalties: Santarus Inc. (San Diego, CA, USA), Cosmo Technologies Ltd (Dublin, Ireland), Tillotts Pharma AG, Wiley-Blackwell Inc. (Hoboken, NJ, USA), Elsevier Ltd (Amsterdam, the Netherlands) and Oxford University Press (Oxford, UK). Simon Travis has received research grants from the following: AbbVie Inc., the International Organization for the Study of Inflammatory Bowel Disease, Eli Lilly and Company, UCB Inc. (Brussels, Belgium), Vifor Pharma, Norman Collisson Foundation (Bicester, UK), Ferring Pharmaceuticals, Schering-Plough, Merck Sharpe & Dohme Corp. (Kenilworth, NJ, USA), Procter and Gamble Ltd, Warner Chilcott Ltd, Abbott Laboratories Ltd, PDL BioPharma Inc. (Incline Village, NV, USA), Takeda UK Ltd and the International Consortium for Health Care Outcomes Measurement. Ailsa Hart reports personal fees from AbbVie Inc., Atlantic Healthcare Ltd (Saffron Walden, UK), Bristol-Myers Squibb, Celltrion Inc. (Incheon, South Korea), Dr Falk Pharma UK Ltd (Bourne End, UK), Ferring Pharmaceuticals, Janssen Pharmaceuticals, Merck Sharpe & Dohme Corp., Napp Pharmaceuticals Ltd (Cambridge, UK), Pfizer Inc., Pharmacosmos A/S (Holbæk, Denmark), Shire Pharmaceuticals UK and Takeda UK Ltd, and non-financial support from Genentech Inc. Alastair Windsor reports personal fees from Takeda, grants from Allergan Inc. (Dublin, Ireland), personal fees from Allergan, personal fees from Cook Medical Inc. (Bloomington, IN, USA) and grants and personal fees from Bard Ltd (Crawley, UK) outside the submitted work. Andrew Plumb reports grants from the National Institute for Health Research (NIHR) Health Technology Assessment (HTA) programme outside the submitted work, grants from the NIHR Fellowships programme during the conduct of the study and honoraria for educational lectures delivered at events arranged by Acelity Inc. (Crawley, UK), Actavis Pharma Inc. (Parsippany-Troy Hills, NJ, USA), Dr Falk Pharma UK Ltd, Janssen-Cilag Ltd (High Wycombe, UK) and Takeda UK Ltd on the subject of inflammatory bowel disease. Ilan Jacobs reports share ownership in General Electric Company (Boston, MA, USA), which manufacturers and sells magnetic resonance imaging equipment. Charles D Murray reports personal fees from AbbVie Inc., Merck Sharpe & Dohme Corp. and Janssen Pharmaceutica outside the submitted work. Antony Higginson reports personal fees from Toshiba Corporation (Tokyo, Japan) outside the submitted work. Steve Halligan reports non-financial support from iCAD Inc. (Nashua, NH, USA) outside the submitted work, and sat on the HTA commissioning board (2008–14). Stephen Morris reports Health Services and Delivery Research (HSDR) Board membership (2014–18), HSDR Evidence Synthesis Sub Board membership (2016), HTA Commissioning Board membership (2009–13) and Public Health Research Board membership (2011–17).