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Increasing evidence has shown that the Covid-19 outbreak, and subsequent school closures and exam cancellations that followed, has impacted adolescent mental health. The current cross-sectional study examined rates of depression, anxiety and Post Traumatic Stress Disorder (PTSD)-like symptoms about Covid-19 in adolescents and whether current or past mental health support, additional support in school, keyworker status, poorer household relationships since the outbreak of Covid-19 or reduced physical activity were associated with elevated levels of depression, anxiety or PTSD-like symptoms. Lastly, it examined perceived changes in mental health due to the Covid-19 pandemic, school closures and the cancellation of exams. A total of 899 adolescents (14-18 years) took part in the 'in isolation instead of in school' (INISS) project. Findings indicated that older adolescents, females, those who currently or previously received mental health support or additional support in school and adolescents who reported poorer relationships at home since Covid-19 were more likely to meet clinical threshold levels for their mental health. Adolescents highlighted worsening of their mental health due to Covid-19 and school closures with mixed positive and negative impact of exam cancellations. Adolescents experiencing clinical threshold levels of depression and anxiety uniquely reported worsening of their mental health since the Covid-19 pandemic, school closures and exam cancellations. Understanding the rates, perceptions and factors associated with increases in depression, anxiety and PTSD-like symptoms in adolescents during the Covid-19 pandemic will inform national policy in supporting adolescent mental health and recovery from the Covid-19 pandemic.