Systems modeling represents an innovative approach for addressing the obesity epidemic at the community level. We developed an agent-based model of the Baltimore City food environment that permits us to assess the relative impact of different programs and policies, alone and in combination, and potential unexpected consequences. Based on this experience, and a review of literature, we have identified a set of principles, potential benefits, and challenges. Some of the key principles include the importance of early and multilevel engagement with the community prior to initiating model development and continued engagement and testing with community stakeholders. Important benefits include improving community stakeholder understanding of the system, testing of interventions before implementation, and identification of unexpected consequences. Challenges in these models include deciding on the most important, yet parsimonious factors to consider, how to model food source and food selection behavior in a realistic yet transferable manner, and identifying the appropriate outcomes and limitations of the model.