One of the most interesting GMO stories in the primary literature: http://www.ncbi.nlm.nih.gov/pubmed/8594427

A gene from Brazil Nuts that coded for a protein high in methionine was cloned into soy plants; soy from the resulting plant caused allergic reactions in subjects.

Had this rolled out globally (at the scale that GMO soy is currently deployed) it probably would have (I'm assuming the paper had all the details correct and did in fact show a causal relationship between the transferred gene and the resulting allergenicity) had an enormous negative health effect.