Many of the plants eaten by farmed ruminants are capable of being genetically modified, and may in the future be modified for nutritional, agronomic or industrial purposes. Techniques are also becoming available for genetic modification of silage and ruminal bacteria. Those working in agricultural biotechnology have a clear responsibility to detect and avoid any unintended or undesirable consequences of such modifications, whether direct or indirect, upon the animal, the consumer and the environment. One of the most general concerns that has been expressed is the possibility for onward transfer of modified gene sequences to gut microorganisms or host cells. Rare acquisition of diet-derived DNA fragments cannot be ruled out, but if this occurs, it must have also occurred throughout mammalian history. The possible impact of genes not normally present in ruminant diets must, however, be considered. Discussion of the use of antibiotic resistance markers in transgene constructs must take into account the wider debate on the likely impact of antibiotic use in animal agriculture on the spread of antibiotic resistant bacteria. There is increasing evidence that overuse of antibiotics has lead to extensive transfer of antibiotic resistance genes between bacteria from the human and animal gut. In general this is likely to have a far greater impact than any rare transfer events involving resistance genes passing from transgenic plants to microbes. Our rapidly improving ability to use sophisticated molecular approaches to predict and track the consequences of genetic modification will help to ensure safe application of GM technology in agriculture in the future.