Since the introduction of genetically modified (GM) crops, the commodity grain system has been under pressure to segregate GM and non-GM crops. Starting at the level of the grain handler, members of the grain supply chain have successfully used quality assurance and identity preservation programs to segregate non GM crops. Producers delivering high-value, identity-preserved crops have become interested in implementing these quality management systems at the farm level. We conduct a cost-benefit analysis that shows that quality assurance program may be profitable for producers, depending on their farm size and equipment management strategy.