BACKGROUND: Despite the high prevalence and negative physical and psychosocial consequences of overweight and obesity in adolescents, very little research has evaluated treatment in this population. Consequently, clinicians working with overweight and obese adolescents have little empirical research on which to base their practise. Cognitive behavioural therapy has demonstrated efficacy in promoting behaviour change in many treatment resistant disorders. Motivational interviewing has been used to increase motivation for change and improve treatment outcomes. In this paper we describe the rationale and design of a randomised controlled trial testing the efficacy of motivational interviewing and cognitive behaviour therapy in the treatment of overweight and obese adolescents. METHODS: Participants took part in a motivational interview or a standard semi-structured assessment interview and were then randomly allocated to a cognitive behavioural intervention or a wait-list control condition. The cognitive behavioural intervention, the CHOOSE HEALTH Program, consisted of 13 individual treatment sessions (12 face-to-face, 1 phone call) followed by 9 maintenance sessions (7 phone calls, 2 face-to-face). Assessments were conducted prior to participation, after the treatment phase and after the maintenance phase of intervention. Improvement in body composition was the primary outcome; secondary outcomes included improved cardiovascular fitness, eating and physical activity habits, family and psychosocial functioning. CONCLUSION: Despite the demonstrated effectiveness of motivational interviewing and cognitive behavioural therapy in the long-term management of many treatment resistant disorders, these approaches have been under-utilised in adolescent overweight and obesity treatment. This study provides baseline data and a thorough review of the study design and treatment approach to allow for the assessment of the efficacy of motivational interviewing and cognitive behavioural therapy in the treatment of adolescent overweight and obesity. Data obtained in this study will also provide much needed information about the behavioural and psychosocial factors associated with adolescent overweight and obesity.