Background Previous brain imaging studies suggested that the brain activity underlying the perception of chronic pain may differ from that underlying acute pain. To investigate the brain regions involved in chronic spontaneous pain due to brachial plexus avulsion (BPA), fluorine-(18)fluorodeoxyglucose (F-18-FDG) positron emission tomography (PET) scanning was applied to determine the glucose metabolic changes in patients with pain due to BPA. Methods Six right-handed patients with chronic spontaneous pain due to left-BPA and twelve right-handed age- and sex-matched healthy control subjects participated in the F-18-FDG PET study. The patients were rated by visual analog scale (VAS) during scanning and Hamilton depression scale and Hamilton anxiety scale after scanning. Statistical parametric mapping 2 (SPM2) was applied for data analysis. Results Compared with healthy subjects, the patients had significant glucose metabolism decreases in the right thalamus and S I (P<0.001, uncorrected), and significant glucose metabolism increases in the right orbitofrontal cortex (OFC) (BA11), left rostral insula cortex and left dorsolateral prefrontal cortex (DLPFC) (BA10/46) (P <0.001, uncorrected). Conclusion These findings suggest that the brain areas involved in emotion, attention and internal modulation of pain may be related to the chronic spontaneous pain due to BPA.