Treatment options and therefore general health in children with congenital heart defects (CHD) improved tremendously over the last decades. Growth is an important marker to evaluate healthy development, especially in patients with chronic diseases. This study aimed to evaluate growth in children with CHD compared to their healthy peers. A retrospective, longitudinal analysis of standardized measurements of height, weight, and head circumference of children with CHD aged 0 to 18 years (n = 18,591) was conducted based on data provided by the German pediatrician network CrescNet. These data were compared to the data of healthy children from the same region. Inclusion was based on the ICD-10 codes for CHD; patients with other growth-altering diseases or medications were excluded. CHD were grouped into mild, moderate, or severe according to their severity. The severity of the CHD influences the height, final height, weight, and head circumference of affected children at birth and in long-term growth. Children with more severe CHD are smaller (− 1 to − 0.7 SDS), lighter (− 1 SDS), and have smaller head circumferences (− 1 SDS) than their healthy peers and children with milder CHD. In a subgroup analysis of children with Down’s syndrome (T21), children with T21 and CHD showed significantly smaller measurements than their peers without CHD. In this subgroup, only the presence but not the severity of the CHD mattered. Despite overall good outcomes and better survival rates, growth as a marker of healthy development in children with CHD may be still impacted and should be closely monitored to offer early intervention.