Herbicide-resistant cropping systems comprise a herbicide-resistant plant and the associated (complementary) herbicide. While herbicide resistance occurs in conventionally bred plants, the trait is mostly produced using genetic engineering methods. Transgenic herbicide-resistant crops are resistant to glyphosate (e.g. 'Roundup') and glufosinate (e.g. 'Liberty' and 'Basta'). Both are full herbicides and are toxic for almost all plants.

Glyphosate inhibits EPSP synthase, an enzyme active in the synthesis of essential aromatic amino acids. Plants are made resistant to glyphosate by transferring to them bacterial genes for either unsensitive EPSP synthase or for an enzyme that breaks down glyphosate. Glufosinate (a herbicide with the chemical name phosphinotricin) blocks the enzyme glutamine-synthase. Blocking the enzyme allows toxic ammonia to build up in the plant's cells, causing the plant to die. To make plants resistant to glufosinate, they receive a bacterial gene (pat or bar) for the enzyme phosphinotricin acetlytransferase (PAT) which acetylises the glufosinate and renders the inhibitor useless.

For about a decade, a heated debate has been underway regarding the costs, risks and uses of herbicide-resistant cropping systems. Proponents argue that they have cut the use of herbicides, something that happened within the first three years of their being introduced in the US – although since 1999, the US has seen a five percent rise in the use of herbicides in soya, cotton and maize, the three main herbicide-resistant crops. Taking in the entire crop-growing period from 1996 to 2004, the US used some 62.7 million kg more herbicides on herbicide-resistant crops compared with conventional management (Benbrook 2004). This did not come as a surprise, as there had been early indications that intensive farming of transgenic herbicide-resistant crops would promote resistance and change the species composition of farmland flora. There are now signs that increasing quantities of complementary herbicides and of two or three other herbicides are needed to combat stubborn weeds in herbicide-resistant crops. Another problem, especially as regards herbicide-resistant rapeseed, is herbicide-resistant volunteers (self-sown plants, mainly fall-out from the previous harvest) which together with wild transgenic rapeseed are a source of spread of transgenes to wild rapeseed and related species. Herbicide-resistant volunteers necessitate the use of additional herbicides or other measures.

The indirect effects of herbicide resistance practices are another aspect that must be taken into account when conducting risk assessments on herbicide-resistant plants. There is a justified suspicion that wide-scale use of herbicides reduces biodiversity in farmland flora and that this effect propagates along the food chain.