OBJECTIVE: In the aftermath of child maltreatment or neglect, the health-related quality of life (HRQoL) in children is likely to be affected. However, research on quality of life in maltreated children is lacking. The aim of this study is to compare the HRQoL in a follow-up sample of children referred to an interdisciplinary hospital child protection team (CPT) to match controls and to explore correlates of HRQoL. METHOD: Of the 319 in- and outpatient children referred to the CPT at the University Children's Hospital Zurich between 2005 and 2006, an eligible sample of 180 children was contacted for a follow-up. HRQoL was assessed for 42 former patients using the self- and proxy-rated KIDSCREEN-27 for children above the age of 6 years and the TAPQOL parent report for children younger than 6 years. HRQoL-scores in the maltreatment group were compared with HRQoL in 39 matched controls. RESULTS: Self-reported HRQoL in maltreated children above the age of 6 years was significantly impaired compared to matched controls. The caregiver-rated HRQoL of maltreated children, however, was not affected. Low socioeconomic status and number of life events were associated with impaired self-reported HRQoL. Analyzed together with these factors, maltreatment lost its predictive power on HRQoL. CONCLUSION: Maltreated children and adolescents suffer from impaired HRQoL even after the maltreatment has been disclosed and targeted by interventions. The impact of socioeconomic environment reinforces the importance of a multidisciplinary and systemic approach to maltreatment as applied by the CPT. Although the nature of discordance between child and caregiver report is not known, researchers and clinicians are strongly encouraged to assess the victim's self-reported HRQoL independently of their proxies' view.