Mindfulness neuroscience is an emerging research field that investigates the underlying mechanisms of different mindfulness practices, different stages and different states of practice as well as different effects of practice over the lifespan. Mindfulness neuroscience research integrates theory and methods from eastern contemplative traditions, western psychology and neuroscience, and from neuroimaging techniques, physiological measures and behavioral tests. We here review several key theoretical and methodological challenges in the empirical study of mindfulness neuroscience and provide suggestions for overcoming these challenges.