Chronic low back pain (CLBP) is now considered a disease of the central nervous system. Two-thirds of individuals with CLBP also have fibromyalgia (FM) which is a chronic pain syndrome characterized by widespread deep musculoskeletal pain and cognitive deficits. The aim of this study was to investigate gray and white matter changes between FM and CLBP groups using vertex analysis of thalamus and tract-based spatial statistics (TBSS). Significant surface depression was detected in right thalamus of patients with FM compare to CLBP. TBSS analysis showed significantly reduced FA in several white matter tracts of patients with FM compared to CLBP.