Acupuncture has been widely used in the West in recent years and demand has been growing for scientific evaluation of its clinical efficacy. The practice of evidence-based medicine has brought new challenges in the design of acupuncture research, and publication of randomized clinical trials on acupuncture has significantly increased. While systematic reviews of these trials have advanced our current knowledge, they have exposed deficiencies in research design and revealed that one design can not answer all research questions. Few clinical studies conducted in China have been published in the West, and most published in Chinese suffer from methodological design flaws that render the results unreliable and unconvincing. Such flaws include inadequate or no randomization, inadequate control, unsatisfactory outcome measurements, lack of proper concealment, insufficient follow-up, and improper statistical analysis. To foster high quality acupuncture clinical research in China, we must cultivate innovation and creativity in research design. It is unwise to simply follow or copy the research methodology of Western pharmaceutical studies. Acupuncture and traditional Chinese medicine (TCM) must be evaluated using rigorous scientific methods that preserve the essence of TCM concepts, so that acupuncture and TCM, these ancient healing arts, can continue to play an important role in the health care systems of modern societies.