Background: In 2007, we commenced the Healthy Beginnings Trial (HBT) Phase 1 study, which is the first randomised controlled trial (RCT) to test the effectiveness of an early childhood obesity intervention in children aged up to 2 years. The results were promising with significant improvements in infant feeding practices and a lower mean body mass index (BMI). The aims of this proposed Phase 2 study are to determine if the early intervention will lead to a lower mean BMI, lower screen time, improved dietary behaviours and demonstrated costeffectiveness of the intervention, in children aged 3½ and 5 years. Methods/design: In Phase 1 of HBT 667 families participated in the RCT. No further intervention will be carried out in HBT Phase 2. In this study the intervention and control groups will be compared for children's outcomes at ages 3½ and 5 years. Primary outcome measures will be 1) BMI, 2) selected dietary measures using a validated survey tool, and 3) physical activity and screen time using a new generation of tri-axial accelerometers. Intention to treat principles will be used in the analysis. Multiple imputation will be used to impute outcomes for subjects lost to follow-up. A cost-effectiveness analysis (CEA) and cost-utility analysis for both HBT Phase 1 and 2 will also be conducted. Discussion: This is the first time that a home-based early intervention strategy has been implemented to prevent the development of childhood obesity and obesity-conducive behaviours. The results of this trial will ascertain whether early intervention during the first 2 years of life is effective and cost-effective in preventing childhood overweight and obesity at 3½ and 5 years old.