Mindfulness training is theorized to lead to a shift in perspective, a so-called “reperceiving”. The observing of inner experiences, thoughts, and emotions leads to a dis-identification from these contents of consciousness, which facilitates exposure and is thought to result in a reduction in emotional reactivity and to more adaptive responding in situations of social threat. This fMRI study investigated whether participation in a Mindfulness-Based Stress Reduction (MBSR) course results in a pattern of neural activation indicative of improved emotion regulation. 28 healthy subjects were quasi-randomized to either an MBSR or a waitlist control group. In a pre-post design, all participants viewed photographs of emotional facial expressions, including angry faces, and labeled the affect of the displayed facial expressions while undergoing fMRI scanning. Data were acquired with a 1.5 T scanner at the Martinos Imaging Center, Massachusetts General Hospital. Activations were analyzed for the angry versus neutral emotional pictures. Results indicated that MBSR participants, but not waitlist control subjects, showed pre-post changes in brain activation that are indicative of improved regulatory control. Furthermore, anatomical MRI scans were analyzed for changes in gray matter concentration due to the MBSR training using voxel-based morphometry. MBSR participants, but not waitlist control subjects, showed pre-post increases in gray matter concentration in the hippocampus, posterior cingulate cortex, temporo-parietal junction and cerebellum. These studies were a first attempt to identify the neural correlates of improved functioning following mindfulness practice.