The effective segregation of specialty grains (waxy maize, high amylase maize, non-GM soybeans) and maize types that are fully approved for food and feed use in the U.S. and Japan, but not yet in the EU at on-farm and commercial grain handling facilities has been the topic of much debate. How can on-farm and commercial systems designed and built to handle large quantities of low value commodities maintain the quality and purity of specialty crops and avoid contamination from genetic traits not desired by certain end users or approved in certain overseas markets? For years producers and commercial operators have been handling maize, soybeans, wheat and other grains in the same receiving systems. Cross contamination is minimized by allowing conveying systems to run empty between loads of different grain types followed by flushing the system of residual grain. According to industry sources, elevator deliveries of maize typically contain less than 0.1 % of soybeans, and deliveries of soybeans typically less than 0.1 % of maize. Thus, why should the same approach not work to maintain the genetic purity of grains and avoid cross-contamination on-farm and at elevators? The inability to successfully segregate multiple grain types is most often related to improper planting sequence and harvest planning, field-to-field pollen drift problems, poor sanitation practices of equipment, human errors during receiving and conveying, lack of trained personnel, poor utilization of available equipment, and poorly designed, maintained and operated equipment. In order to minimize the contamination potential and maximize quality, operators need to implement a strict cleanout program for each piece of equipment, field operation planning, or use dedicated equipment. Existing handling systems nd equipment can be successfully used to maintain quality and purity as long as the same attention to detail is paid as to segregating maize from soybeans and vice versa.