Abstract Background There are growing worldwide concerns about the ability of primary health care systems to manage the major burden of illness in young people. Over two thirds of premature adult deaths result from risks that manifest in adolescence, including injury, neuropsychiatric problems and consequences of risky behaviours. One policy response is to better reorientate primary health services towards prevention and early intervention. Currently, however, there is insufficient evidence to support this recommendation for young people. This paper describes the design and implementation of a trial testing an intervention to promote psychosocial risk screening of all young people attending general practice and to respond to identified risks using motivational interviewing. Main outcomes: clinicians’ detection of risk-taking and emotional distress, young people’s intention to change and reduction of risk taking. Secondary outcomes: pathways to care, trust in the clinician and likelihood of returning for future visits. The design of the economic and process evaluation are not detailed in this protocol. Methods PARTY is a cluster randomised trial recruiting 42 general practices in Victoria, Australia. Baseline measures include: youth friendly practice characteristics; practice staff’s self-perceived competency in young people’s care and clinicians’ detection and response to risk taking behaviours and emotional distress in 14–24 year olds, attending the practice. Practices are then stratified by a social disadvantage index and billing methods and randomised. Intervention practices receive: nine hours of training and tools; feedback of their baseline data and two practice visits over six weeks. Comparison practices receive a three hour seminar in youth friendly practice only. Six weeks post-intervention, 30 consecutive young people are interviewed post-consultation from each practice and followed-up for self-reported risk taking behaviour and emotional distress three and 12 months post consultation. Discussion The PARTY trial is the first to examine the effectiveness and efficiency of a psychosocial risk screening and counselling intervention for young people attending primary care. It will provide important data on health risk profiles of young people attending general practice and on the effects of the intervention on engagement with primary care and health outcomes over 12 months. Trial registration ISRCTN16059206