Special segregations that provide unique qualities for end use products are being specified by buyers. As users of wheat become more specific about quality, the number of quality segregations that the logistical pipeline must accommodate increases. The additional cost of increased grain segregations will influence the optimal level of wheat variety segregations marketed in a supply chain. The primary objective of this research is to develop a model that captures the logistical costs of increased grain segregations in the marketing system. A simulation model was developed to add logistical uncertainty in demand, receipts, rail deliveries, and transit time. Sensitivities were conducted on certain variables to determine their effects on logistical costs. Logistical costs increase as more segregations are added. In addition, increasing uncertainty into the system raises logistical costs. Pipeline configuration also affects costs as the number of categories/storage bins present at origin may differ from the wheat categories demanded or the number of storage bins present at the export elevator.