Chronic low back pain (CLBP) is now considered a central nervous system disease. Thalamus is a key relay station for processing and transmission of nociceptive information to the cerebral cortex. We used vertex-based morphometry and connectivity-based diffusion tractography to test the hypothesis that the CLBP is associated with altered thalamic shape and altered white matter integrity of the thalamic projections to cortical regions in frontal and parietal lobes. Compare to controls, CLBP exhibited significant surface depression in left thalamus and lower fractional anisotropy in left thalamic projections to the posterior parietal cortex. This may represent a degenerative pain-related process.