Complementary and alternative medicine use is increasing in both the general population and in individuals with chronic illness. A significant proportion of adult and pediatric patients with inflammatory bowel disease use or have used complementary and alternative medicine as determined by multiple surveys conducted in North America, Europe and Australia. There was a heterogenous selection of complementary and alternative medicine therapies chosen by patients, with variations due to geography and age. However, in general, their use is sought due to frustration with conventional therapies and the perceived safety of complementary and alternative medicine therapies. One of the dilemmas that arises when assessing the topic of complementary and alternative medicine use is rapidly changing definitions of what is and what is not considered conventional medicine. With our increasing understanding of the intricacies of the gastrointestinal immune system and host-microflora interactions, determining a scientific basis behind many complementary and alternative medicine therapies in vitro or in vivo is leading to evaluation of these therapies in humans. This will require well-designed and rigourously conducted clinical trials with sufficient sample size.