Background: The prevalence of mental illness in young people is the highest of any age group, with the onset of depression, anxiety and substance use peaking between 18 and 24 years. Effective treatments that target sub-threshold or mild to moderate levels of disorder in young people are required to reduce the risk of persistence and recurrence. The aims of this study are to evaluate whether treatments that are less intensive than cognitive-behaviour therapy, such as problem solving therapy and exercise treatments, are acceptable and effective in managing depression and anxiety symptoms in young people and to identify possible attributes in those who are likely to respond to these treatments.Methods/design: This is a factorial randomised controlled trial conducted at a large, metropolitan youth mental health service. Participants are young help-seekers aged 15-25 years with sub-threshold or mild to moderate levels of depression and anxiety (with or without comorbid substance use). The interventions comprise 4 treatment combinations delivered by psychologists over 6 sessions on a weekly basis: a psychological intervention (problem solving therapy versus supportive counselling) and an exercise intervention (behavioural exercise versus psychoeducation). Structured assessments occur at baseline, mid-point, end-point (6 weeks) and at a 6- and 12-month follow-up. The primary outcomes are depression and anxiety symptoms as measured by the Beck Depression and Anxiety Inventories. Secondary outcomes include remission (defined as no longer meeting the diagnostic criteria for a disorder if threshold level was reached at baseline, or no longer scoring in the clinical range on scale scores if sub-threshold at baseline), substance use, and functioning.Discussion: The effectiveness of less complex psychological and exercise interventions in young help-seekers with sub-threshold or mild to moderate presentations of high prevalence disorders is yet to be explored. This study has been designed to examine the effectiveness of these interventions delivered alone, or in combination, in a youth-specific service. If effective, the interventions have the potential to prevent the progression of early symptoms and distress to later and potentially more serious stages of mental disorder and reduce the likelihood of ongoing problems associated with the risk of persistence and recurrence. Trial registration: Australian New Zealand Clinical Trials Registry ACTRN12608000550303. © 2011 Parker et al; licensee BioMed Central Ltd.