In the past, concerns about farm animal welfare have mainly related to husbandry systems, with much less attention given to the effects of breeding. Over the years selective breeding programmes have led to great increases in productive output and efficiency in farm livestock, particularly poultry, pigs and dairy cattle. These species have also become increasingly specialised for a specific function such as producing eggs, meat or milk. But there is strong evidence that in many cases where there is a narrow focus on improving production, these selective breeding programmes are associated with serious welfare costs (Rauw et al., 1998), despite the existence of legislation that, in theory, prohibits such a situation. The European Directive on farm animal welfare (Directive 98/58/EC) states that: ‘No animals shall be kept for farming purposes unless it can reasonably be expected, on the basis of their genotype or phenotype, that they can be kept without detrimental effect on their health or welfare.’ Negative effects of selective breeding on welfare are due to over-emphasis on production traits in relation to other aspects of the animal’s biology. The animal is ‘genetically pre-programmed’ to allocate a disproportionately large amount of resources to the particular production trait (such as producing a large breast muscle or huge quantities of milk), often at the expense of the rest of the body’s functions. The biological balance of the animal is disturbed, with much of the body’s emphasis on particular traits. In their report on the welfare of chickens (2000), the European Commission’s Scientific Committee on animal health and animal welfare concluded that: ‘…the major welfare problems in broilers are those which can be regarded as side effects of the intense selection mainly for growth and feed conversion. ’ Animals selected on the basis of production often maintain high output whatever the cost to them. For example, high yielding dairy cows may continue to produce milk even when in negative energy balance. Body reserves will be mobilised to allow milk production to continue which, if prolonged, can lead to health and fertility problems (Pryce et al., 2002).