We report two cases of ammonium acid urate stones that could not be diagnosed by dual-energy computed tomography (CT). Case 1: A 37-year-old female was referred to our hospital for a left kidney stone. She had a medical history of anorexia nervosa, Basedow's disease and hypoparathyroidism. Her height was 167 cm, weight 38 kg and body mass index (BMI) 13. 6. CT showed a left kidney stone measuring 18×12 mm. Dual-energy CT showed that the left kidney stone was composed of uric acid. Chemolysis by oral administration of alkaline citrate was attempted. Six months later, CT showed no improvement, and endoscopic combined intrarenal surgery (ECIRS) was performed. Stone analysis revealed pure ammonium acid urate. Case 2: A 42-year-old female was referred to our hospital because of right back pain. She had a medical history of ventricular septal defect and urolithiasis. Her height was 158 cm, weight 37 kg, and BMI 14.8. CT showed a right kidney stone measuring 16×12 mm. Dual-energy CT showed that the right kidney stone was composed of uric acid. Chemolysis by oral administration of alkaline citrate was attempted. Two months later, CT showed no improvement, and ECIRS was performed. Stone analysis revealed pure ammonium acid urate. It is difficult to differentiate uric acid stones and ammonium acid urate stones by dual-energy CT. Even when dual-energy CT suggests uric acid stones, ammonium acid urate stones should also be considered in thin young women and women with a history of anorexia nervosa.