The World Trade Organization Sanitary and Phytosanitary Agreement (SPS Agreement) relies heavily on science and expert organizations to avoid and resolve trade disputes over measures enacted under the rationale of food safety or plant and animal health protection. However, the state of science for sanitary and phytosanitary risk analysis is highly uncertain, and the SPS Agreement leaves many science policy issues unsettled. The international agencies charged under the SPS Agreement with harmonizing standards and forging international scientific consensus face a daunting and politically-charged task. Two case studies are briefly developed. In the first case, the international scientific consensus strongly supports the U.S. challenge of the European Union's ban on cattle growth hormones, but the root causes of the dispute go much deeper. The case suggests that establishing a precedent for SPS measures based solely on "sound science" may be a slippery objective. In the second case, domestic avocado producers challenged a U.S. Department of Agriculture assessment which concluded that a partial lifting of the ban on Mexican avocado imports posed a negligible plant pest risk. Although the Department's phytosanitary risk assessment gained endorsement by independent scientists, a contributing factor to resolving this dispute was the threat of retaliation against U.S. agricultural exports to Mexico. A recent survey of current and proposed technical barriers to U.S. agricultural exports suggests that the trade impacts could approach $5 billion a year and that the most common SPS disputes in the future will be over biological hazards--particularly plant pests and foodborne microbial pathogens. This poses a tremendous challenge, however, because the practice of risk assessment for biological stressors is much less developed than that for chemical substances. The paper concludes with some proposed criteria for evaluating the weight of scientific evidence in SPS risk assessment.