BackgroundChildhood obesity gives rise to health complications including impaired musculoskeletal development that associates with increased risk of fractures. Prevention and treatment programs should focus on nutrition education, increasing physical activity (PA), reducing sedentary behaviours, and should monitor bone mass as a component of body composition. To ensure lifestyle changes are sustained in the home environment, programs need to be family-centered. To date, no study has reported on a family-centered lifestyle intervention for obese children that aims to not only ameliorate adiposity, but also support increases in bone and lean muscle mass. Furthermore, it is unknown if programs of such nature can also favorably change eating and activity behaviors. The aim of this study is to determine the effects of a 1 y family-centered lifestyle intervention, focused on both nutrient dense foods including increased intakes of milk and alternatives, plus total and weight-bearing PA, on body composition and bone mass in overweight or obese children.Methods/designThe study design is a randomized controlled trial for overweight or obese children (6–8 y). Participants are randomized to control, standard treatment (StTx) or modified treatment (ModTx). This study is family-centred and includes individualized counselling sessions on nutrition, PA and sedentary behaviors occurring 4 weeks after baseline for 5 months, then at the end of month 8. The control group receives counselling at the end of the study. All groups are measured at baseline and every 3 months for the primary outcome of changes in body mass index Z-scores. At each visit blood is drawn and children complete a researcher-administered behavior questionnaire and muscle function testing. Changes from baseline to 12 months in body fat (% and mass), waist circumference, lean body mass, bone (mineral content, mineral density, size and volumetric density), dietary intake, self-reported PA and sedentary behaviour are examined.DiscussionThis family-centered theory-based study permits for biochemical and physiological assessments. This trial will assess the effectiveness of the intervention at changing lifestyle behaviours by decreasing adiposity while enhancing lean and bone mass. If successful, the intervention proposed offers new insights for the management or treatment of childhood obesity.Trial registrationClinicalTrials.gov, NCT01290016.