BackgroundFood system function is vulnerable to disruption from a variety of sources. Disruption of the processes required for food provision may result in decreases in food security in affected communities. Currently, there are few tools that quantitatively predict or analyze food system vulnerabilities to contribute to food system resilience analysis. This work presents a prototype version of one such tool, a fault tree, which can be used conceptually and for future modeling work. Fault tree analysis is an engineering tool used to illustrate basic and intermediate factors that can cause overall system failures.MethodsThe fault tree defines food system functioning as food security at the community level and maps the components of the food system onto three main tenets of food security – accessibility, availability, and acceptability. Subtrees were populated using a top down approach guided by expertise, extant literature, and 36 stakeholder interviews.ResultsThe food system is complex, requiring 12 subtrees to elaborate potential failures. Subtrees comprising accessibility include physical accessibility of the vending point and economic accessibility among community members. Food availability depends on the functioning of the food supply chain, or, in the case of individuals who rely on donated food, the food donation system. The food supply chain includes processing, wholesale operations, distribution systems, and retail center subtrees. Elements of acceptability include the medical appropriateness, nutritional adequacy, and cultural acceptability of food. Case studies of the effects of Winter Storm Jonas of 2016 and the 2013–2017 California drought in Baltimore City illustrate the utility of the fault tree model.ConclusionFTA of potential routes to food system failure provides a tool that allows for consideration of the entirety of the food system; has potential to provide a quantitative assessment of food system failure and recovery; and is able to capture short-term and long-term hazards in a single framework. This systems modeling approach highlights an extensive list of vulnerability points throughout the food system, and underscores the message that reducing food system vulnerabilities requires action at all levels to protect communities from the risks of short-term and long-term threats to food security.Electronic supplementary materialThe online version of this article (10.1186/s12889-018-5563-x) contains supplementary material, which is available to authorized users.