The technology of genetically modified foods (also called GM foods) allows selection of an specific genetic trait from one organism and introduces it in the genetic code of the food source through genetic engineering techniques. This has made possible to develop food crops with specific beneficial traits and elimination of undesirable traits in others. In spite of the great agricultural advantages of transgenic crops these do not have acceptance in some countries because: a) the suspicious of consumer as result of allergic reactions observed with some transgenic crops, b) the lack of worldwide regulations to these crops, and c) the negative side effects to environment by the massive farming of transgenic crops, for example loss of genetic diversity, creation of higher adapting weeds, the migration of transgenic genes to their wild relatives and less likely migration of transgenic genes to other unrelated organisms by horizontal transference. Also, the contamination of food with transgenic residues has persuaded different countries to restrict importation of food made with transgenic plants or labelling food or ingredients as or from transgenic crops. There are worrying aspects about the effect of transgenic food over human health such as: 1) many of transgenic genes used today have never been present in human diet, making impossible to know the effect that they will cause, 2) the allergic potential of some proteins codified by some transgenic genes, and 3) in the genetic engineering of crops, many times a gene with antibiotic resistance is included like selectable gene, having the possibility that this gene migrates to pathogen bacteria that affect the health of plants, human and animal, developing bacterial resistance to those antibiotics making hard to have bacterial control. In the present work, literature is reviewed in order to present a perspective about some of the above concerns. In addition, are presented results of different studies in order to answer the following questions: a). Do DNA and proteins are degraded during the traditional soybean food processing?, b). Does food processing affect the persistence of transgenic residues? and c) Does is possible to develop more efficient techniques for detection of transgenic residues in soybean-based foods?