The authors review the work of the previous Scientific Committee on Animal Health and Animal Welfare and the current European Food Safety Authority (EFSA) in providing scientific advice on the welfare aspects of animal transport and the impact of this advice on the European Union (EU) regulatory framework. Through its Protocol on the Protection and Welfare of Animals, the Treaty of Amsterdam obliges European institutions to pay full regard to the welfare requirements of animals when formulating and implementing EU legislation. Regulation 1/2005 states that EU legislation should be amended to take into account new scientific evidence. Provisions for poultry, cats and dogs take into account the recommendations included in EFSA's Scientific Opinion which considers different species (poultry, deer, rabbits, dogs and cats, fish and exotic animals). Examples of the effect of the scientifically based conclusions and recommendations from the Scientific Opinion on the measures in Regulation 1/2005 are summarised and show the impact of scientific evidence on EU legislation.