The aim of this study was to investigate renal function and injury in infants and young children with congenital heart disease (CHD). We prospectively enrolled 58 CHD children aged a parts per thousand currency sign3 years and 20 age-matched controls and divided these into four groups: Group I, acyanotic CHD (n = 24); Group II, cyanotic CHD with arterial oxygen saturation of > 75 % (n = 20); Group III, cyanotic CHD with arterial oxygen saturation of a parts per thousand currency sign75 % (n = 14); Group IV, normal controls (n = 20). Urinary levels of microalbumin (MA), N-acetyl--D-glucosaminidase (NAG), and alpha 1-microglobulin (alpha 1-MG) corrected by creatinine (UCr) were compared. Children with CHD had elevated urinary alpha 1-MG/UCr levels, with Group III children having the highest level. Groups I and III children had higher urinary NAG/UCr levels than those of Groups II and IV. Urinary MA/UCr levels in the three patient groups were comparable and significantly higher than that in the control group. A alpha 1-MG x 100/ (alpha 1-MG + MA) of < 15 %, indicative of glomerular damage, was present in two patients in Group I and one in Group III, but none in Group II. Tubular injury can occur in CHD patients during infancy and early childhood. Among our patient cohort, it was most prominent in children with severe cyanosis. Glomerular injury was detected in some individuals with advanced heart failure or severe cyanosis.