This study assesses newly qualified doctors' confidence in practising clinical skills related to the assessment and management of mental health conditions and how this correlates with other areas of medicine. We conducted a national survey of 1311 Foundation Year 1 doctors in the UK. Survey items assessed confidence recognising mentally unwell patients, conducting a mental state examination, assessing cognition and mental capacity, formulating a psychiatric diagnosis and prescribing psychotropic medications. A substantial proportion of surveyed doctors lacked confidence in their clinical skills related to mental health and prescribing psychotropic medications. Network analysis revealed that items corresponding to mental health were highly correlated, suggesting a potential generalised lack of confidence in mental healthcare. We identify areas of lack of confidence in some newly qualified doctors' ability to assess and manage mental health conditions. Future research might explore how greater exposure to psychiatry, integrated teaching and clinical simulation might better support medical students for future clinical work.