Partial and intermittent pelvi-ureteric junction obstruction (PUJO) can potentially confound the diagnosis of upper tract obstruction. We report the case of a gentleman who received a renal graft from his sister. The donor kidney had a box-shaped extra-renal pelvis, which showed unobstructed drainage on the diuretic renogram. However, it manifested in the recipient as PUJO, and he needed pyelo-native ureterostomy for deteriorating graft function. The purpose of this report is to highlight a seemingly innocuous entity in the donor that may manifest in the recipient with significant consequences on graft function. It also discusses the appropriate timing of intervention in these cases.