Production and processing of genetically modified organisms (GMO) in line with the European food safety and labelling regulations lead to an elevated risk of unintentional GMO contamination in food producing and processing companies. For these companies GMO contamination can lead to extensive losses such as decreased product value, recall expenses or decreased brand equity. The question that occurs in many food producing and processing companies is how to manage the risk of GMO contamination most effectively. The objective of this paper is to show how food companies manage the risk of GMO contamination. Because of the complexity of the German food sector the analysis focuses on one supply chain namely: the production, processing and trading of maize and maize products. Within this supply chain an assessment of potential losses and safety measures was conducted in a two-step analysis. At first personal interviews with executives or quality managers of companies along the whole supply chain were carried out. Then the results of these interviews were analyzed and used to create the framework for a second session of formalized online interviews within companies of the maize chain. The results of the survey in maize producing, processing and trading, companies show the risk of potential losses that can occur in case of GMO contamination. Additionally the results show the safety measures that can effectively reduce the risk of GMO contamination.