The use of complementary and alternative medicine (CAM) continues to grow in the United States. The Agency for Healthcare Research and Quality has devoted a substantial proportion of the Evidence-based Practice Center (EPC) program to systematic reviews of CAM. Such syntheses present different challenges from those conducted on western medicine topics, and in many ways are more difficult. We discuss 3 challenges: identifying evidence about CAM, assessing the quality of individual studies, and addressing rare serious adverse events. We use illustrations from EPC evidence reports to show readers approaches to the 3 areas and then present specific recommendations for each issue.