Currently the agriculture based on biotechnology is developing very dynamically, similarly to organic farming system. While considering different aspects of co-existence between GM and non-GM products (both conventional and the organic ones) it should be taken into account that no form of agriculture, neither conventional or organic nor the GMO based, should be excluded, and that the ability to maintain diversified agricultural production system is a precondition for providing a high degree of choice for consumers. In this context co-existence between GM and non-GM products has a big impact on both economic and market issues. However, a modified management system within the whole value supply chain is necessary to secure proper conditions for the co-existence between GM and non-GM products. In case of some food and feed products this chain has already been international in its scope. Although the co-existence between GM and non-GM products is determined by economic factors, the attitudes of consumers towards these products should be considered a key issue of development of value supply chains based on different agricultural systems.