A 6 year old boy developed hyperammonaemic encephalopathy following a subureteric injection for treatment of vesicoureteric reflux. The hyperammonaemia may be explained by a postoperative urinary tract infection with a urea splitting organism, leading to raised urine ammonia that was absorbed easily across a dilated urinary tract. Agitation and alteration in consciousness level following a urological procedure, in a child with a dilated urinary tract, may be signs of a treatable hyperammonaemic encephalopathy.