Genetically modified (GM) grains have increased in importance. Moving biotech grains from producers to processors is a challenge for the grain handling system that could involve increased segregations. The objective of this research is to determine how testing strategies affect the logistical costs of a grain pipeline when GM wheat is present. A logistical model was developed and simulated to analyze impacts of uncertainty in demand, receipts, test accuracy, rail deliveries, and transit time. Sensitivities were conducted on certain variables to determine their effects on logistical costs. Analysis revealed that logistical costs are impacted by the number of quality categories and uncertainties in the system. Adding GM grains increased costs due to testing requirements and increased segregation demands as the number of wheat categories rises.