Mindfulness is currently attracting a great deal of attention as a psychotherapy technique. It is defined as bringing one's complete attention to the experiences occurring in the present moment in a nonjudgmental or accepting way. The Five Facet Mindfulness Questionnaire (FFMQ) was developed to assess individual differences in mindfulness states. The FFMQ is composed of five facets representing elements of mindfulness: non-reactivity to inner experience, non-judging, acting with awareness, describing, and observing. In the present study, we applied voxel-based morphometry to investigate the relationship between the brain structure and each facet as measured by the FFMQ. The results showed a positive association between the describing facet of mindfulness on the FFMQ and gray matter volume in the right anterior insula and the right amygdala. In conclusion, mindfulness was related with development in parts of the somatic marker circuit of the brain.