Background: Magnetic resonance enterography (MRE) is an established tool to evaluate for changes associated with inflammatory bowel disease (IBD), but has not been studied in sub-clinical IBD. We sought to evaluate the use of MRE in children with spondyloarthritis (SpA), who are at risk of having sub-clinical gut inflammation.Methods: Children with juvenile idiopathic arthritis (JIA) with evidence of intestinal inflammation as evidence by an abnormal fecal calprotectin assay were offered MRE of their intestines. Flavored sports drink containing polyethylene glycol 3350 was used as oral contrast. Glucagon was used to arrest peristalsis. Patients were imaged in the prone position on a 1.5 T scanner. Heavily T2-weighted fat-suppressed coronal and axial images using breath-hold technique were obtained, followed by post-gadolinium fat-suppressed T1-weighted gradient echo images.Results: We recruited five children with juvenile idiopathic arthritis (JIA); four had SpA, and one had poly-articular JIA. All five had evidence of intestinal inflammation based upon a positive fecal calprotectin assay and successfully completed the MRE. Three of the studies showed findings suggestive of IBD, including thickening and contrast uptake at the terminal ileum (TI) in one child, contrast uptake of the distal ileum in another, and prominent vasa recta and mesenteric lymph nodes in the third. The child with evidence of inflammatory changes at the TI underwent colonoscopy, which revealed inflammatory bowel disease limited to the TI.Conclusions: MRE can be used to evaluate for subclinical IBD in children with JIA. This protocol was safe and well-tolerated, and identified mild changes in three of the subjects. © 2012 Stoll et al; licensee BioMed Central Ltd.