There is good agreement between MR enterography and bowel ultrasound with regards to disease location and activity in paediatric inflammatory bowel disease.

•There is good agreement between ultrasound and MRI in paediatric IBD.•Fewer technical difficulties were reported with ultrasound than MRI.•Using histology as the gold standard, both MRI and US show high specificity.•We find ultrasound is well tolerated in children and advocate its use.