In contrast to the increasing use of GM plants in world-wide agriculture, the acceptance of GM food is still low in the European Union (EU). In order to ensure freedom of choice for consumers and users of GM and non-GM products, GM food and feed products have to be labeled in case a tolerance threshold of 0.9 % is exceeded for EU authorized GMOs. This paper aims to quantify the cost of traceability and co-existence systems for GM food from the seed to the food level for sugar, wheat starch and rapeseed oil for human consumption in Germany respecting the 0.9 % threshold for labelling of GM food. The cost calculation for traceability and co-existence measures follows the principle of aggregating all incurred cost on the different levels of the value chain and to increase the price of the final product at each level. Altogether the measures to ensure co-existence and traceability lead to 5 % to 13 % higher price for GMO-free rapeseed oil, to 2 % to 5 % higher prices of GM-free sugar and to 8 % price increase for GMO-free wheat starch.