Purpose VACTERL association is a rare and complex condition of congenital malformations, often requiring repeated surgery and entailing various physical sequelae. Due to scarcity of knowledge, the study aim was to investigate self-reported health-related quality of life (HRQoL), anxiety, depression and self-concept in children and adolescents with VACTERL association and self-reported anxiety and depression in their parents. Methods Patients aged 8-17 years with VACTERL association and their parents were recruited from three of four Swedish paediatric surgical centres during 2015-2019. The well-established validated questionnaires DISABKIDS, Beck Youth Inventories, Beck Anxiety Inventory and Beck Depression Inventory were sent to the families. Data were analysed using descriptives, t tests and multivariable analysis. Results were compared with norm groups and reference samples. Results The questionnaires were returned by 40 patients, 38 mothers and 33 fathers. The mean HRQoL was M = 80.4, comparable to children with asthma (M = 80.2) and diabetes (M = 79.5). Self-reported psychological well-being was comparable to the norm group of Swedish school children, and was significantly higher than a clinical sample. Factors negatively influencing children's HRQoL and psychological well-being were identified. The parents' self-reports of anxiety and depression were comparable to non-clinical samples. Conclusions Although children and adolescents with VACTERL association reported similar HRQoL to those of European children with chronic conditions, their psychological well-being was comparable to Swedish school children in general. Nevertheless, some individuals among both children and parents were in need of extra support. This attained knowledge is valuable when counselling parents regarding the prognosis for children with VACTERL association.