Genetically modified grains have rapidly become popular among producers across U.S. Some consumers, particularly in the EU, South Korea, and Japan, are unwilling to purchase products containing ingredients from genetically modified or transgenic crops. This paper develops a model to represent costs of segregating non-transgenic grains at country elevators and simulates these costs at representative elevators in South Dakota under alternative scenarios employing a case study approach. The overall cost of segregating non-transgenic grains under a zero rejection rate ranged from 1.5 to 21.7, 1.2 to 11.3, and 1.3 to 16.4 cents per bushel, for corn, soybeans, and wheat, respectively.