Modern biotechnology has dramatically increased our ability to alter the agronomic traits of plants. Among the novel traits that biotechnology has made available, an important group includes Bacillus thuringiensis-derived insect resistance. This technology has been applied to potatoes, cotton, and corn. Benefits of Bt crops, and biotechnology generally, can be realized only if risks are assessed and managed properly. The case of Starlink corn, a plant modified with a gene that encodes the Bt protein Cry9c, was a severe test of U.S. regulatory agencies. The U.S. Environmental Protection Agency had restricted its use to animal feed due to concern about the potential for allergenicity. However, Starlink corn was later found throughout the human food supply, resulting in food recalls by the Food and Drug Administration and significant disruption of the food supply. Here we examine the regulatory history of Starlink, the assessment framework employed by the U.S. government, assumptions and information gaps, and the key elements of government efforts to manage the product. We explore the impacts on regulations, science, and society and conclude that only significant advances in our understanding of food allergies and improvements in monitoring and enforcement will avoid similar events in the future. Specifically, we need to develop a stronger fundamental basis for predicting allergic sensitization and reactions if novel proteins are to be introduced in this fashion. Mechanisms are needed to assure that worker and community aeroallergen risks are considered. Requirements are needed for the development of valid assays so that enforcement and post market surveillance activities can be conducted.