Studies have shown that honey often contains traces of genetically modified organisms. Since the flight radius of bees is several kilometres wide, there is high danger that the bees collect the pollen of genetically modified plants and thus impurify the honey.

In May 2008, the administrative court of Augsburg ruled that honey containing pollen of the genetically modified corn 810 is no longer marketable. Since MON810 is only licensed as animal feed but not as food, beekeepers are neither allowed to sell genetically "contaminated" honey, nor to give it away as a present; rather, they have to make sure it is disposed of.

In September 2011, the European Court of Justice (ECJ) ruled in the so-called honey ruling that pollen in honey is an ingredient (and not a natural component) and that honey containing pollen from genetically modified organisms is subject to the labelling regulations for genetically modified foods. But in January 2014, the European Parliament approved a change of the so-called honey directive, according to which pollen is to be regarded a natural component of honey and not an ingredient. Consumer protection associations and particularly beekeeper associations criticized the decision.