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AIM To report the initial experiences with functional cine magnetic resonance urography (cine MRU) and assess its usefulness as a novel postoperative evaluation method of ileal ureter substitution. MATERIALS AND METHODS The medical records of 17 patients from who underwent cine MRU during June 2010 to December 2019 during their follow-up after ileal ureter substitution were collected. The cine MRU videos of reconstructive urinary tract were observed, and the luminal diameter, contraction ratio, peristaltic waves, and ureteral jets were measured. RESULTS Seventeen patients underwent cine MRU after ileal ureter substitution during their follow-up. Based on their cine MRU videos assessing the morphology and the peristaltic motility of the reconstructive urinary tract, there was resolution of preoperative hydronephrosis, which matched their ameliorative renal function. Clearly, peristaltic motility of the ileal graft was observed in 14 patients with obvious peristaltic waves and ureteral jets. CONCLUSION This study is the first to assess the clinical utility of functional cine MRU during the patient follow-up after ileal ureter substitution. Cine MRU is a radiation-free, non-invasive imaging method that can clearly show the morphology and the peristaltic motility of the ileal graft. Therefore, cine MRU, as a novel technique, will be extremely useful in the postoperative evaluation of patients after ileal ureter substitution.