GM foods are controversial for two reasons:
First, there is the worry that the genetic modification could also introduce unwanted traits to the organism as well as the desired ones, creating a health risk. All GM food undergoes a rigorous safety assessment before it can be sold in the EU. This includes checks for any changes in its allergenic potential and nutritional profile, and is carried out by the European Food Safety Authority, EFSA.
The second concern is the risk of crops becoming cross-contaminated. Fields where GM crops are grown have to sit within a ‘quarantine’ zone where non-GM strains of the same crop cannot be grown, to prevent contamination with the GM strain. However, this is difficult to control, and some cross-contamination would be inevitable if GM crops were ever grown on a large scale in Europe. While this would be a problem for organic farmers, it is debatable whether there would be any real risk for consumers.