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Background: United States pediatric guidelines recommend that childhood obesity counseling be conducted in the primary care setting. Primary care-based interventions can be effective in improving health behaviors, but also costly. The purpose of this study was to evaluate the cost of a primary care-based obesity prevention intervention targeting children between the ages of two and six years who are at elevated risk for obesity, measured against usual care., Methods: High Five for Kids was a cluster-randomized controlled clinical trial that aimed to modify children's nutrition and TV viewing habits through a motivational interviewing intervention. We assessed visit-related costs from a societal perspective, including provider-incurred direct medical costs, provider-incurred equipment costs, parent time costs and parent out-of-pocket costs, in 2011 dollars for the intervention (n = 253) and usual care (n =192) groups. We conducted a net cost analysis using both societal and health plan costing perspectives and conducted one-way sensitivity and uncertainty analyses on results., Results: The total costs for the intervention group and usual care groups in the first year of the intervention were $65,643 (95% CI [$64,522, $66,842]) and $12,192 (95% CI [$11,393, $13,174]). The mean costs for the intervention and usual care groups were $259 (95% CI [$255, $264]) and $63 (95% CI [$59, $69]) per child, respectively, for a incremental difference of $196 (95% CI [$191, $202]) per child. Children in the intervention group attended a mean of 2.4 of a possible 4 in-person visits and received 0.45 of a possible 2 counseling phone calls. Provider-incurred costs were the primary driver of cost estimates in sensitivity analyses., Conclusions: High Five for Kids was a resource-intensive intervention. Further studies are needed to assess the cost-effectiveness of the intervention relative to other pediatric obesity interventions.