Background Hypothyroidism with impairment of renal function and raised creatinine phosphokinase (CPK) is described in adults and children with acquired hypothyroidism, but not in congenital hypothyroidism. Case presentation A male infant born at term weighing 3390 g was seen aged 2 months with prolonged jaundice. Examination showed somnolence, umbilical hernia, enlarged fontanelles and lower limb edema; length 55 cm (-1.5 SD), weight 5.4 kg (-0.13 SD). Biochemistry showed fT4 < 1 pmol/L, TSH = 1044.36 mu UI/mL, creatinine 77 mu mol/L(normal <35 mu mol/L), estimated glomerular filtration rate (GFR) 26 ml/min/1.73 m(2), CPK 3952.5 IU/L (normal<400 IU/L). Ultrasound showed no thyroid tissue in the neck. In view of the renal impairment, peritoneal dialysis was initially contemplated but postponed and the child received levothyroxine 10 mu g/kg/day. Two months later thyroid function tests, CPK and renal function had all normalized with creatinine 19 mu mol/L and GFR 116 ml/min/1.73m(2). Discussion Reversible renal impairment is attributable to severe congenital hypothyroidism causing decreased myocardial contractility and cardiac output and to a direct effect on the kidneys. Thyroid function should be checked in infants with renal impairment of unknown cause. Cautious fluid management is indicated in hypothyroid infants. Hypothyroidism may also be associated with elevated serum CPK levels but resolves with thyroxin therapy.