BACKGROUND Post-traumatic stress disorder (PTSD) is often characterized by region-specific brain activation/deactivation and functional abnormalities in corticolimbic circuitry, as elucidated by task-dependent functional neuroimaging. However, little is known about the abnormalities in the local coherence of cortical and subcortical activity occurring during the resting state. OBJECTIVE To evaluate the functional discrepancy of local coherence between cortical and subcortical regions in PTSD patients using resting-state functional magnetic resonance imaging (fMRI). METHODS Resting-state fMRI (RS-fMRI) was performed on 14 outpatients with PTSD, along with 14 age- and sex-matched normal control subjects. Regional homogeneity (ReHo), a measurement of the coherence of spontaneous RS-fMRI signal oscillations within spatially neighboring voxels, was examined. RESULTS Compared with the normal controls, PTSD patients showed increased local coherence in subcortical regions, including amygdala, hippocampus, thalamus, and putamen, and decreased local coherence in cortical regions, including medial prefrontal cortex and dorsolateral prefrontal cortex. Moreover, a correlation analysis of the ReHo measurement versus the severity of the disorder was performed, and highly positive correlation were observed in the right amygdala. CONCLUSIONS The present study identified a functional discrepancy of local coherence between cortical and subcortical regions in PTSD patients compared with normal controls. The findings revealed that resting-state abnormalities might lead to further improvement of the understanding of the neural substrates of cognitive impairment and symptoms in PTSD.