Traditional Chinese medicine encompasses many different practices, most notably acupuncture and moxibustion. Traditionally, these modalities are used in combination to augment treatment but seldom are they tested together in clinical studies. Numerous acupuncture studies have been conducted in Asia, Europe, and the United States but there have been few randomized controlled trials utilizing moxibustion outside of East Asia. Limited studies have described the use of a moxibustion control or placebo procedure. The methods for developing an acupuncture and moxibustion protocol used in a randomized controlled trial for irritable bowel syndrome, diarrhea predominant in adults are described here. Our approach conformed to the scientific rigor for a clinical trial and was consistent to the foundations of traditional Chinese medicine.