Obesity prevention in young children is a public health priority. In the USA, nearly 10% of children less than 5 years of age are obese, and most attend some form of out-of-home child care. While a number of interventions have been conducted in early care and education settings, few have targeted the youngest children in care or the less formal types of child care like family child care homes. Additionally, only two previous studies provided recommendations to help inform future interventions. Methods This paper presents lessons learned from two distinct intervention studies in early care and education settings to help guide researchers and public health professionals interested in implementing and evaluating similar interventions. We highlight two studies: one targeting children ages 4 to 24 months in child care centres and the other intervening in children 18 months to 4 years in family child care homes. We include lessons from our pilot studies and the ongoing larger trials. Results To date, our experiences suggest that an intervention should have a firm basis in behaviour change theory; an advisory group should help evaluate intervention materials and plan for delivery; and realistic recruitment goals should recognize economic challenges of the business of child care. A flexible data collection approach and realistic sample size calculations are needed because of high rates of child (and sometimes facility) turnover. An intervention that is relatively easy to implement is more likely to appeal to a wide variety of early care and education providers. Conclusions Interventions to prevent obesity in early care and education have the potential to reach large numbers of children. It is important to consider the unique features and similarities of centres and family child care homes and take advantage of lessons learned from current studies in order to develop effective, evidence-based interventions. (author abstract)