Although farmers may experience decreased pesticide costs and higher revenues attributed to herbicide-tolerant and insect-resistant crops, there are costs. Genetically engineered seed costs are greater than traditional seed, and farmers are also required to pay a technology fee. The costs to the environment are even greater. In most cases herbicide-resistant crops bring about an increase in herbicide use and result in environmental problems. Also when a single herbicide is used repeatedly on a single crop, the chances of herbicide resistance developing greatly increase and the dosages of herbicides may increase as well. Though, glyphosate is said to have benefits reducing non-point scource runoffs, it has been found to be toxic to soil nontarget fauna. Bacillus Thuringiensis (BT) is engineered into crops to control pests such as caterpillars and mosquitoes however, no assessments of its true effects on the environment and nontarget organisms have been made. This is one of the genetically engineered toxins that have possible detrimental effects on our environment. Little research has been conducted concerning the impact of BT on aquatic systems and the scavengers that might feed on the engineered plants(Paoletti and Pimintel, 1995).

Genetically modified food is a huge threat to the loss of biodiversity. Diversity is the basis of ecological stability. Monoculture crops are genetically uniform, and therefor notoriously prone to disease and pest outbreaks. According to an FAO report, by the year 2000, the world will have lost 95% of the genetic diversity utilized in agriculture at the beginning of this century. Under the monopoly of genetic manipulators intellectual property rights, the livelihoods of small farmers will be further compromised, by both seed royalties and by restrictive practices of seed certification. At the same time, the use of non-toxic herbicides with herbicide resistant crops will result in irretrievable losses of indigenous agricultural and natural diversity.

It is also important to understand that genes function in an extremely complex, interconnected network, so that ultimately, the expression of each gene depends on that of every other. That is why organisms will tend to change in non-linear, unpredictable ways, even when a single gene is introduced. It is dangerous to manipulate genes when one cannot predict all the possible detrimental effects of their future. Because no gene ever functions in isolation, there will almost always be unexpected and unintended side effects" from the gene or genes transferred into an organism. The risk involved with gene manipulation is too great when considering the lack of sufficient understanding of all the possible side effects of genetic modifications(Ho,Dr.Mae-Wan, 1998).