Background: The onset of chronic kidney disease (CKD) is an important prognostic factor in young adults with congenital heart disease (CHD). Although it is likely that CKD is manifest early in CHD patients, the prevalence among adolescents is still unknown. The National Kidney Foundation’s Kidney Disease Improving Global Outcomes guidelines 2012 recommend new equations for the estimated glomerular filtration rate (eGFR) and highlight the importance of albuminuria for CKD screening. The objective of the present study was to estimate the prevalence of CKD in CHD adolescents. Methods: This observational cross-sectional study included 115 patients aged 10–18 years attending the cardiologic outpatient clinic at our institution as a follow-up after cardiac surgery in infancy related to various CHDs. CKD assessment used the CKD criteria 2012, including eGFR equations based on serum creatinine and cystatin C, and measurement of albuminuria. Results: No patient had an eGFR <60 mL min<sup>–1</sup> 1.73 m<sup>–2</sup>. However, 28.7% of all patients (95% CI 20.7–37.9) had eGFR<sub></sub>between 60 and 89 mL min<sup>–1</sup> 1.73 m<sup>–2</sup> when estimated by the bedside Schwartz creatinine-based equation,<sup></sup>and 17.4% (95% CI 11.2–24.1) had eGFR<sub></sub>between 60 and 89 mL min<sup>–1</sup> 1.73 m<sup>–2</sup> when estimated by the Zappitelli equation, combining creatinine and cystatin C. Of all patients, 20.0% (95% CI 12.1–26.7) had orthostatic proteinuria, and none had persistent albuminuria. Conclusions: There was no evidence of CKD in the present population aged 10–18 years. The significance of an eGFR between 60 and 90 mL min<sup>–1</sup> 1.73 m<sup>–2</sup> is not concordant for this age range and requires further investigations.