Current Western therapies for many gastrointestinal diseases are suboptimal and potentially toxic. The majority of patients with digestive diseases are turning to complementary and alternative medicine for symptom relief and improved quality of life, due to dissatisfaction with conventional medical therapies. There is emerging evidence that many of these complementary and alternative medicine modalities are highly effective in modulating the immune system, disrupting the proinflammatory cascade and restoring digestive health while improving patients' quality of life. We present evidence to support the potential utility of complementary and alternative medicine modalities for irritable bowel syndrome and inflammatory bowel disease. For each condition, we detail the proposed mechanisms of action and explore the current data for the prevention and/or treatment of disease.