Abstract Background Most mental health disorders begin before the age of 18, peaking at 14.5 years (Solmi, 2022) and manifest as emotional and behavioural difficulties that are more frequent in institutional social care (ISC): former foster care recipients have higher rates of depression and PTSD than the general population (Pecora, 2009). The rate of children living in residential care facilities in Europe and Central Asia is double the global average (UNICEF, 2024). This study aims to assess and compare the mental health of children in ISC centers and regular high schools. Methods A cross-sectional study was conducted in ISC centres and high schools in 2022-2023. The sample size consisted of children aged 11-17 living in ISC (n = 49) or in families (n = 193). Online anonymous survey was applied to assess the prevalence of endured violence, substance use and measure mental health outcomes using the Strengths and Difficulties Questionnaire (SDQ-25). Results A total of 242 respondents (age mean 14.6, SD = 2.12) in ISC and families showed similar poor mental health rates (42% and 44%, respectively). Prosocial behaviour problems were exhibited more by boys (p < 0.05), whereas emotional symptoms were more common in families (p < 0.001): 90% normal SDQ-25 scores in ISC vs 60% in families. Enduring psychological (38% vs 60.2%) violence was more prevalent among children in families (p < 0.05); smoking - in ISC, alcohol use - in families (p < 0.05). In both groups enduring physical violence was associated with smoking and alcohol use (p < 0.05), and overall poor SDQ-25 results strongly correlated (p < 0.001, r = 0.815, r = 0.610, respectively) with hyperactivity. Conclusions A significant part of study participants reported poor mental health outcomes with most problems in relationships with peers. Mental health risk factors such as violence or substance abuse are associated with poor emotional wellbeing while being more common among children living with families. Key messages • Children living in ISC and in families demonstrate similar level of mental health problems. • Varying prevalence of substance abuse among children living in different settings highlights the importance of environmental factors when addressing the issue.