Food allergies affect up to 8% of children in the United States and may occasionally lead to severe life-threatening reactions. Because there is currently no cure for food allergies, strict avoidance of the allergen-containing foods is the only means of preventing an allergic reaction. Consumers rely on food manufacturers to reliably track and declare the presence of food allergens in products. Over the past 10 to 20 years, the food industry has increasingly adopted allergen control approaches in its processing facilities. However, the major industry costs related to food allergen management have not been fully described. The objective of this study was to characterize the factors that contribute to the economic impact of food allergen control practices on the food industry. A focus group (n = 100) was conducted with food industry professionals to identify key areas of cost for food allergen management. A survey based on the domains identified was then developed and disseminated to a convenience sample (n = 50) of quality control food industry specialists with knowledge of their company's food allergen management practices. Nearly all companies (92%) produced food products containing one or more of the top eight allergenic foods recognized by the U.S. Food and Drug Administration or sesame seeds. Cleaning procedures, employee training, and the potential for a recall due to allergen cross-contact were most frequently rated as the important factors in food allergen management. Recalls due to food allergen cross-contact, cleaning procedures, equipment and premises design, and employee training were ranked as the greatest allergen management expenses. Although 96% of companies had a food allergen control plan in place, nearly half (42%) had at least one food allergen-related recall within the past 5 years. The industry appears to endorse a willingness to unify precautionary allergen labeling to communicate a clear message more effectively to consumers.