Background: Nephropathy is a well-known complication of congenital heart disease (CHD), and the risk of developing renal impairment is particularly high in patients with cyanotic CHD. Most investigations of renal impairment in CHD have involved patients 20 years and older. This study investigated renal tubule function in pediatric patients with CHD, and compared findings in cyanotic and acyanotic groups. Methods: Twenty children with acyanotic CHD, 23 children with cyanotic CHD, and 13 healthy children were enrolled. Blood and early morning urine samples were collected from each subject to measure urinary concentrations of sodium, microalbumin, creatinine, β<sub>2</sub>-microglobulin, and N-acetyl-β- D-glucosaminidase (NAG). Results: The age and sex distributions in the three groups were similar. Median fractional excretion of sodium (FeNa) and urinary NAG/creatinine were significantly higher in the cyanotic group than in the control group (p = 0.022 and p = 0.002, respectively). There were no statistically significant differences among the groups with respect to urinary β<sub>2</sub>-microglobulin/creatinine, urinary microalbumin/creatinine or glomerular filtration rate. Conclusion: Tubular injury can be detected before glomerular injury occurs even within the first decade of life in patients with cyanotic CHD.