In conventional plant breeding, little attention has been paid to the possible impacts of new plant varieties on food safety or the environment. Nonetheless, this kind of breeding has sometimes caused negative effects on human health. For instance, a cultivated crop variety created by conventional cross breeding can contain excessive levels of naturally occurring toxins.

The introduction of genetically modified plants has raised some concerns that gene transfer could occur in the field between cultivated and wild plants and such concerns also apply to conventional crops.

The potential impacts of conventionally bred crops on the environment or on farmers' traditional varieties have generally not been subjected to regulatory controls. Some of the concerns of gene transfer between domesticated and wild plants that have arisen because of the introduction of genetically modified plants also apply to conventional crops.

Prior to the advent of genetic engineering, plant breeding was not subject to a great deal of regulation. Seed certification standards ensure the purity and quality of seeds, but little attention has been paid to the possible food safety or environmental impacts of new plant varieties derived from conventional breeding.

Conventional plant breeding differs considerably from natural selection. Natural selection creates resilient biological systems; it ensures the development of an organism that contains properties that adapt it to a variety of environmental conditions and ensure continuation of the species. Artificial selection and conventional plant breeding break down precisely these resilient systems, thereby creating gene combinations that would rarely survive in nature.

Conventional breeding has been responsible for a few cases of negative effects on human health. In one case a potato cultivar was found to contain excessive levels of naturally occurring toxins, and in another case a celery cultivar conventionally bred for high insect resistance caused a skin rash if harvested by hand without protection.

Most of the world's major food crops are not native to their major production zones; rather, they originated in a few distinct “centers of origin” and were transferred to new production areas through migration and trade. Highly domesticated plants are grown all over the world and migration outside cultivated areas has only rarely caused a serious problem. Even when grown in their center of origin, as with potatoes in South America or maize in Mexico, hybrids between cultivated and wild species have not been permanently established. There are several reports of gene flow between cultivated plants and their wild relatives but in general this has not been considered a problem.

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