We developed a new MRI mini-capsule marker device to measure whole gut transit (WGTT) in pediatric constipation to overcome image quality and ionizing radiation limitations of current X-ray methods. Thirty five healthy children and 16 patients with constipation were asked to swallow a number of mini-capsules and imaged, following a common X-ray radiopaque marker protocol. The capsules were imaged successfully in the colon. WGTT was calculated from the capsules count and was significantly longer in the patients compared to the controls. The study also showed excellent feasibility and safety of using the new device and methods in children with constipation.