This study aims to characterize the psychological wellbeing of chronic headache (CH) patients, to identify cortical structural abnormalities and any associations of those abnormalities with resting state functional connectivity (rsFC), and to determine whether such rsFC abnormality is specific to CH patients. Compared with healthy controls (CONCH), CH patients suffered from mild depression, sleep disturbances, and relatively poor quality of life. CH patients also exhibited widespread cortical thickness (CT) abnormalities in left premotor (BA6), right primary somatosensory (S1) and right prefrontal (BA10) cortices, as well as in regions of default mode and executive control networks. Using cortical regions with thickness abnormality as seeds, we found cortical region pairs showed strengthened rsFC in CH patients. Using the same seeds, rsFC analysis from chronic low back pain (CLBP) patients and their controls (CONCLBP) identified abnormalities in non-overlapping cortical region pairs. Direct comparison of rsFC between CH and CLBP patients revealed significantly differences in thirteen cortical region pairs, including the four identified in CH and CONCH comparison. Across all three groups (CH,CLBP and CON), the rsFC between left multisensory association area (BA39) and left posterior cingulate cortex (BA23) differed significantly. Eight regions showed CT abnormality in CLBP patients, two of which overlapped with those of CH patients. Our observations support the notion that CH and CLBP pain are pathological conditions, under which the brain develops distinct widespread structural and functional abnormalities. CH and CLBP groups share some similar structural abnormalities, but rsFC abnormalities in several cortical region pairs appear to be pathology-specific. (C) 2017 Wiley Periodicals, Inc.