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The use of complementary and alternative medicine (CAM) by patients with inflammatory bowel disease (IBD) is common. Physicians and scientists believe that the randomized controlled trial (RCT) provides the best evidence of an intervention's efficacy. However, there are only a few controlled trials that have assessed these therapies in IBD and all contain methodological problems. The RCT does not always fit well with the underlying principles of disease causation and treatment of CAM. Many forms of CAM take a holistic approach to the diagnosis and treatment of disease, where the patient plays an active and key role in healing and treatments are often highly individualized. Therefore, the use of placebos, blinding, and random allocation to structured treatment protocols in an RCT setting is often contradictory to the principles of CAM. We still know relatively little about the use of CAM in IBD. Prior to embarking upon a program of clinical trials to evaluate these therapies, a better understanding of the specific therapies being used, reasons for their use, and their potential side effects is required. We also need to understand how the CAM practitioners use their therapies, what they view as the appropriate indications, and how treatments are best administered.