The pathophysiology of chronic abdominal symptoms in Crohn’s disease (CD) is complex. Recent pilot data using automated quantification of motility MRI suggests reduced variation in apparently normal bowel may underpin symptoms, including pain and diarrhoea. This two-centre validation study tests this association and compares automated measurements with subjective radiologist bowel motility assessment. We confirmed that reduced spatial variation of motility is significantly associated with the severity of abdominal symptoms, although the correlation was not strong. Automated measurement had superior inter-reader variability than subjective radiologist assessment, and showed a stronger association with patient symptoms.