Measures are being developed and implemented enabling the co-existence of conventional, genetically modified (GM) and organic cropping systems. In order to segregate GM from conventional crops in the entire supply chain, a food or feed company has to reorganise its production. This may involve for dedication of the production line to non-GM, or production can be organised on the same plant, using spatial or temporal segregation. In practice, only the latter method is used in the feed industry, as no investments in new machinery are necessary in the case. The segregation and identity preservation of GM and non-GM crops has to be well organised. An important tools used to proof the identity of the imported raw materials is the batch or product declaration and in some cases, a supplementary certificate of analysis for the raw materials is provided. In compound feed production, specific procedures to reduce carry-over are introduced and described in a book of charge, such as rinsing of transportation and production line, empty declaration of transport systems or storage bins and specific discharge and production orders. All these measures however imply supplementary costs to the manufacturer. A major additional cost is the price difference between GM and non-GM raw materials. Other extra costs result from losses in flexibility, a devaluation of the rinsing product, analysis and audits. As a result, the cost of a compound feed using non-GM is higher than with GM. Benefits to the segregation measures are an increased gamut of products and an improved organisation and management of the production. Together with an improved traceability system, consumers’ confidence is also increased.