Pediatric primary care is an important setting in which to address obesity prevention, yet relatively few interventions have been evaluated and even fewer have been shown to be effective. The development and evaluation of cost-effective approaches to obesity prevention that leverage opportunities of direct access to families in the pediatric primary care setting, overcome barriers to implementation in busy practice settings, and facilitate sustained involvement of parents is an important public health priority. The goal of the Healthy Homes/Healthy Kids (HHHK 5-10) randomized controlled trial is to evaluate the efficacy of a relatively low-cost primary care-based obesity prevention intervention aimed at 5 to 10year old children who are at risk for obesity. Four hundred twenty one parent/child dyads were recruited and randomized to either the obesity prevention arm or a Contact Control condition that focuses on safety and injury prevention. The HHHK 5-10 obesity prevention intervention combines brief counseling with a pediatric primary care provider during routine well child visits and follow-up telephone coaching that supports parents in making home environmental changes to support healthful eating, activity patterns, and body weight. The Contact Control condition combines the same provider counseling with telephone coaching focused on safety and injury prevention messages. This manuscript describes the study design and baseline characteristics of participants enrolled in the HHHK 5-10 trial.