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Objective To evaluate the functional outcome of anatrophic nephrolithotomy in children. Patients and methods All children undergoing anatrophic nephrolithotomy for complex branching and multiple renal calculi over an 11‐year period were studied prospectively. Demographic data, treatment details and outcome, as assessed by X‐ray, ultrasonography and isotope studies, were recorded. Anatrophic nephrolithotomy was carried out with surface cooling of the kidney followed by nephrostomy drainage for 5–7 days. Results Nine children (median age 4 years, range 7 months to 9 years) underwent anatrophic nephrolithotomy. Predisposing factors included urinary tract infection (by Proteus mirabilis) in all and hyper‐calciuria in two children. The median (range) total ischaemic time at operation was 25 (15–40) min and the operative duration 150 (120–200) min. Three children required a blood transfusion. Stone clearance was incomplete in one child. There was no recurrent stone formation after a long‐term follow‐up (median 32 months, range 14–107) in the other patients. Isotope studies showed impaired split renal function (<40%) in six children before surgery; there was a significant decline (>5%) in divided function in five children (range 6–16%) after surgery. Conclusion Anatrophic nephrolithotomy is an effective means of rendering children with branching calculi stone‐free, but this study suggests that it leads to some further parenchymal damage. [ABSTRACT FROM AUTHOR]