Background. Studies have shown that a proportion of children as young as two years are already overweight. This indicates that obesity prevention programs that commence as early as possible and are family-focused are needed. This Healthy Beginnings Trial aims to determine the efficacy of a community-based randomized controlled trial (RCT) of a home visiting intervention in preventing the early onset of childhood overweight and obesity. The intervention will be conducted over the first two years of life to increase healthy feeding behaviours and physical activity, decrease physical inactivity, enhance parent-child interaction, and hence reduce overweight and obesity among children at 2 and 5 years of age in the most socially and economically disadvantaged areas of Sydney, Australia. Methods/design. This RCT will be conducted with a consecutive sample of 782 first time mothers with their newborn children. Pregnant women who are expecting their first child, and who are between weeks 24 and 34 of their pregnancy, will be invited to participate in the trial at the antenatal clinic. Informed consent will be obtained and participants will then be randomly allocated to the intervention or the control group. The allocation will be concealed by sequentially numbered, sealed opaque envelopes containing a computer generated random number. The intervention comprises eight home visits from a specially trained community nurse over two years and pro-active telephone support between the visits. Main outcomes include a) duration of breastfeeding measured at 6 and 12 months, b) introduction of solids measured at 4 and 6 months, c) nutrition, physical activity and television viewing measured at 24 months, and d) overweight/obesity status at age 2 and 5 years. Discussion. The results of this trial will ascertain whether the home based early intervention is effective in preventing the early onset of childhood overweight and obesity. If proved to be effective, it will result in a series of recommendations for policy and practical methods for promoting healthy feeding and physical activity of children in the first two years of life with particular application to families who are socially and economically disadvantaged.