In this paper we develop a framework of analysis for the main economic issues that arise in the pursuit of system of labelling for GM and non-GM products under the introduction of GM products. This model represents a vertical relationship with three stages in the supply chain: manufacturer, retailer and final consumers. Co-mingling may occur between non-GM and GM products: contaminated non-GM products may be sold on the final market. To avoid this, the retailer induces his supplier to make tests before the sale. The retailer accepts lots if the GM content is under the public labelling threshold. Above the threshold, lots are sold by the manufacturer on a GM market. Public regulation takes the form of the purity threshold or labelling threshold. The impact of the firm’s strategies takes the form of the effort (segregation measures) and the sampling size set up by the supplier/manufacturer. The paper aims to determine under what conditions demand for non-GM products can be satisfied, given that upstream coexistence generates admixture risks, thereby resulting in (i) additional segregation and control tests and (ii) a risk of downgrading for non-GM due to this potential mixing. With this model, not only are the prices and quantities of commercialized non-GM products analyzed, but also the level of contamination of non-GM products throughout the supply chain. An analysis is proposed to evaluate impacts of private and public policies on stakeholders’ trade-offs and on the GM/non-GM coexistence.