All in all the theory behind the science is good: it is a natural technological progression to make plants better through genetic modelling. But unfortunately there are a few side effects and problems associated:

Very often for no apparent reason the incorporated gene falls silent after a while. Or conversely, genes that were silent are activated because the new gene interferes with the regulatory devices of the other genes. This is because putting in a new gene is not that precise and it could end up at different positions. This might result in new unknown toxic substances being produced by the plant. Unpredictable side effects are called pleiotropic effects. This could be decreased fertility or a colour change in a plant or animal. For example potatoes were made resistant to one kind of bug, but at the same time became vulnerable to other kinds of insects.

New Scientist

The great problem is that very often it works well in the test tube, as it is designed to work there, but in nature it might function in a different way.

People with food allergies are at great risk, as they might be allergic to the gene that has been introduced. Preventive measures are taken so as to avoid using genes from common food allergy sources and it should be indicated on the product that it is genetically modified and which genes are used.

To find out more on how safe these foods are go to the following link:
http://www.cfsan.fda.gov/~dms/fdbioeng.html