Although preclinical and clinical data strongly support an association between the amygdala and chronic pain by the presence of mood and cognitive disturbances in affected individuals, little attention has been paid to morphometric measurement of the structure in patients with chronic low back pain (CLBP). In the present study, magnetic resonance volumetric and surface analysis, using FMRIB's integrated registration and segmentation tool (FIRST), were performed to compare structural magnetic resonance imaging data obtained from 33 patients with CLBP with those obtained from 33 demographically similar healthy control individuals. Our results indicated that the normalized volumes of the left and right amygdala were significantly smaller in the CLBP group than in the control group. Detailed surface analyses further localized these differences. The degree of volume reduction was different between the left and right amygdala, with a greater involvement of the left side. Both groups exhibited similar significant hemispheric asymmetry for the amygdala (left > right). Similar asymmetry was suggested in the subgroup of 24 unmedicated patients. No significant correlations were found between amygdala volumes and pain characteristics or depressive symptoms. Our study provides in vivo imaging evidence of abnormal morphology of the amygdala in patients with CLBP using a fully automated segmentation method.Our study found that patients with CLBP had statistically significantly smaller normalized volumes of the bilateral amygdala, compared with healthy control individuals, with a greater involvement of the left side. These results may help to characterize the impaired affective-cognitive dimension in patients with chronic pain.