To assess the health-related quality of life (QoL) in children with congenital heart diseases (CHD) with a validated questionnaire in comparison with control children. We prospectively recruited 282 children with CHD aged from 8 to 18 years in two tertiary care centers (France and Belgium) and 180 same-age controls in randomly selected French schools. Children's QoL was self-reported with the KIDSCREEN-52 questionnaire and reported by parents with the KIDSCREEN-27. QoL scores of each dimension were compared between CHD and controls and between the classes of disease severity. Both centers were comparable for most demographic and clinical data. Age- and gender-adjusted self-reported QoL scores were lower in CHD children than in controls for physical well-being (mean ± SEM 45.97 ± 0.57 vs 50.16 ± 0.71, p < 0.0001), financial resources (45.72 ± 0.70 vs 48.85 ± 0.87, p = 0.01), peers/social support (48.01 ± 0.72 vs 51.02 ± 0.88, p = 0.01), and autonomy in the multivariate analysis (47.63 ± 0.69 vs 49.28 ± 0.85, p = 0.04). Parents-reported scores were lower in CHD children for physical (p < 0.0001), psychological well-being (p = 0.04), peers/social support (p < 0.0001), and school environment (p < 0.0001) dimensions. Similarly, the disease severity had an impact on physical well-being (p < 0.001), financial resources (p = 0.05), and peers/social support (p = 0.01) for self-reported dimensions, and on physical well-being (p < 0.001), psychological well-being (p < 0.01), peers/social support (p < 0.001), and school environment (p < 0.001) for parents-reported dimensions. However, in multivariate analysis on self-reported QoL, disease severity was significantly associated with the self-perception dimension only. Self-reported QoL of CHD children was similar to that of same-age healthy children in seven of 10 dimensions, but parents-reported QoL was impaired in four of five dimensions.