Objective To evaluate the clinical effect of Quyu Huazhuo decoction using iontophoresis delivery on nonalcoholic fatty liver disease (NAFLD) .Methods One-hundred-and-twenty-four patients with NAFLD were enrolled in the clinical trial and divided into four treatment groups: n=32, Quyu Huazhuo decoction (200 ml bid po) delivered by the iontophoresis HD-91-II instrument with electrical stimulation acupuncture (Beijing Hongbo Technology Development Corp.) ;n=30, Quyu Huazhuo decoction (200 ml bid po) without the iontophoresis instrument;n=31, iontophoresis instrument treatment only, with no drug delivery;n=31, Polyene Phosphatidylcholine (Essentiale) capsules (456 mg tid po) .After eight weeks, the effective rate of each treatment modality for NAFLD was assessed by comparing changes in symptoms and biochemical indexes.Results There was no statistically significant difference in the effective rates for the groups treated with the Quyu Huazhuo decoction with or without the iontophoresis instrument (P>0.05) .However, the effective rates of both Quyu Huazhuo decoction treated groups were higher than those of the iontophoresis instrument only and the Polyene Phosphatidylcholine-treated group (P<0.05) .The symptoms of all four groups improved after eight weeks of therapy (vs.pre-treatment, P<0.05) .While the serum alanine aminotransaminase (ALT) and total cholesterol (CHO) levels were significantly reduced (all vs.pre-treatment, P<0.05) there="" was="" no="" significant="" changes="" to="" the="" triglyceride="" levels="" all="" p="">0.05) .The Polyene Phosphatidylcholine-treated group showed the most extensive reduction of ALT (vs.all other groups, P<0.05) .The Quyu Huazhuo decoction plus iontophoresis instrument-treated group showed the most extensive reduction of CHO (vs.all other groups, P<0.05) .Conclusion Quyu Huazhuo decoction treatment with the iontophoresis instrument is more effective for treating NAFLD than Quyu Huazhuo decoction treatment alone or treatment with the Western medicine Polyene Phosphatidylcholine (Essentiale) .