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To study the effect of the storage of urine in intestinal reservoirs on long‐term renal function and the possible causes of deterioration.Eighty‐seven patients (aged 4–35 years) with bladder exstrophy who underwent reconstruction of the lower urinary tract using a bowel segment were enrolled in a prospective protocol. The glomerular filtration rate (GFR) was measured before and after surgery at 1, 2, 5 and 10 years using 51Cr‐ethylenediamine tetra‐acetic acid. Patients with a decline in GFR of > 5% were investigated to identify the cause.Of 58 patients with a follow‐up of ≥ 10 years, 53 were evaluable, four having been lost to follow‐up and one refusing to accept the protocol. In these 53 patients, the mean (SD) GFR decreased from 97.9 (20.4) to 92.9 (23.6) mL/min/1.73 m2 (P = 0.24). However, this decrease was accounted for by 10 patients (19%) whose GFR fell by ≥ 20% over the 10 years. The causes of renal deterioration in these 10 patients were; chronic retention and/or infection caused by inadequate catheterization in poorly compliant patients (five), uretero‐ileal stenosis (one), a high‐pressure reservoir (one) and uncertain causes (three).For 80% of the patients, the storage of urine in intestinal reservoirs did not change renal function for at least 10 years. However, ≈ 20% of patients had some deterioration in renal function during the 10‐year follow‐up, usually from identifiable and remediable causes. The storage of urine in bowel does not appear to be inherently damaging to kidney function. Patients with an enterocystoplasty need regular monitoring of renal function; when deterioration is detected the urinary tract must be functionally assessed.