Chronic pain and depression are common diseases and result in intense suffering and form a huge burden for society. They are difficult to treat, especially when occurring together. We studied the effectiveness of Mindfulness Based Cognitive Therapy (MBCT) to alleviate pain and depressions in patients suffering from both chronic pain and active depression. Furthermore, we investigated the effects of MBCT on body awareness and brain structure- and functional connectivity. To do so 40 patients were by chance assigned to either continue their regular treatment or in addition to participate in MBCT. Measurements were taken before and after the intervention. Participating in MBCT resulted in decreased depression severity but not in reduced pain. Furthermore, we found that MBCT resulted in increased body awareness. Interestingly, the positive effects of MBCT on depression were in part due to increase in body awareness. Preliminary analyses of the brain scans suggest that MBCT resulted in normalization of depression related abnormalities in brain structure and connectivity. These findings are important as they suggest that MBCT is effective for depression in patients with chronic pain. Furthermore, they provide an insight in possible treatment mechanisms, namely normalization of emotion-regulation related brain abnormalities and increased body awareness.