Functional gastrointestinal (GI) diseases are common and there are patients who are refractory to medical therapies as not all treatments work in all patients. Consequently, a large number of patients with functional GI diseases use complementary and alternative medicine, such as acupuncture or electroacupuncture (EA). In this issue, Zheng et al. reported interesting results of a multi-center placebo-controlled clinical study on the use of EA for treating refractory functional dyspepsia; another study reported a multi-center clinical trial on EA for chronic functional constipation; Liang et al. studied mechanisms of EA involving enteric nervous system and neurotransmitters in treating constipation in rats. While controversial reports are available in the literature, EA with appropriate methodologies as shown in these recent studies is believed to be effective in treating certain functional GI diseases. In this mini-review, a number of clinical studies, including those included in this issue on the use of EA for treating gastro-esophageal reflux, functional dyspepsia, irritable bowel syndrome, and constipation are reviewed. Some critically important issues, such as the choice of stimulation parameters for EA, the administration frequency of the therapy, and the appropriate choice of placebo for clinical research are also discussed. Mechanisms of action involved in the therapeutic effects of EA for gut dysmotility and future research directions are also presented.