There is a long tradition of treating GI disorders with acupuncture. The aetiology (origin) of many GI disorders is complicated, in many cases nothing to do with the stomach itself, so it makes sense that a system like acupuncture can be effective when western medicine struggles.
Unlike western medicine, acupuncture treats the whole person, not just an isolated symptom. Thus something like GI disorders, which can often have causes that are difficult to pin down, can respond well to treatment.
The acupuncture therapist will assess the entire patient's health before beginning treatment. The key to successful treatment is to isolate and treat blockages in the flow of Qi, or universal energy.
Qi flows along meridians, channels that lie just beneath the skin, and is essential for good health. With key acupuncture points relating to each of the major organs, including the liver, the stomach and the spleen, the therapist is able to treat these organs from a remote location.
Once the flow of Qi has been unblocked, the body is able to use its own natural powers to heal itself. In the long run this is much more effective than simply taking some medication. Often times medications simply block the symptoms rather than dealing with the underlying cause.
Thus when treated with medication, problems can often re-occur. By treating the underlying cause, and restoring the body's overall good health, problems can be resolved in the long term.
In addition to using needles, your therapist may also use other techniques such as herbal medicine, and moxibustion (the burning of herbs), plus recommend changes in diet.