OBJECTIVE: To compare the efficacy and side effects of bilateral globus pallidus internus (GPi) and subthalamic nucleus (STN) deep brain stimulation (DBS) in the same patient with primary dystonia. METHODS: Patients with primary dystonia from the department of functional neurosurgery in Beijing Tiantan Hospital were recruited for the study. Four electrodes were bilaterally implanted in the GPi and STN. A trial stimulation was applied to determine the preliminary therapeutic effects. Five evaluations were conducted: preoperative, postoperative (before stimulation), after sham stimulation, and after stimulation for 24 hours of GPi and STN using optimal parameters, judged by the Burke-Fahn-Marsden Dystonia Rating Scale (BFMDRS). RESULTS: The BFMDRS movement score decreased after both short-term GPi stimulation (from 15.3 +/- 6.9 to 7.6 +/- 4.2, P < 0.05) and short-term STN stimulation (from 15.3 +/- 6.9 to 8.6 +/- 5.0, P < 0.05). There were significant reductions in facial (eyes and mouth) movement scores after short-term GPi and STN DBS compared with baseline (P < 0.05), but not in cervical symptoms (P > 0.05). The cervical symptoms of tonic dystonia had an improvement after long-term DBS treatment (P < 0.05). There were more adverse events with STN DBS; however, most side effects could be ameliorated by adjusting stimulation parameters. CONCLUSIONS: Both short-term GPi and STN stimulation improved the motor symptoms of dystonia, but there was no significant difference between GPi DBS and STN DBS. There were more side effects associated with STN stimulation.