We present a rare case of Klinefelter syndrome who presented with perinatal ascites, unilateral renal agenesis and a prostatic utricle cyst. The patient was born at term via emergency Caesarean section with gross abdominal distension. Antenatally, amniocentesis revealed a fetal karyotype of Klinefelter syndrome (47, XXY), and the 34-week ultrasound scan showed a cyst measuring 17×21×27 mm located inferior–posterior to the bladder. There was no ascites noted then, but a small left pelvic kidney was present. Ultrasound kidney, ureter and bladder as well as CT scan of the thorax, abdomen and pelvis done at birth showed a solitary right kidney with large-volume ascites and no evidence of a cyst adjacent to the bladder. These findings suggest urinary ascites from an involuting left renal system or a ruptured prostatic utricle cyst. We report the first case of Klinefelter syndrome associated with a prostatic utricle cyst and unilateral renal agenesis, presenting with neonatal ascites.