The concept of science-based rules for the establishment of trade barriers was a new development that arose from the Uruguay Round. It is an attempt to de-politicise decision making in the complex areas of human, animal and plant health as well as aspects relating to the environment. In the short time it has been in operation it has become a mantra for some but an anathema to others with an interest in trade policy. It is now at the heart of a major trade dispute between the EU and the United States over trade in the products of biotechnology. The paper discusses the controversies relating to the science-based system and provides suggestions to improve its efficacy.