The beneficial clinical effects of mindfulness practices are receiving increasing support from empirical studies. However, the functional neural mechanisms underlying these benefits have not been thoroughly investigated. Some authors suggest that mindfulness should be described as a 'top-down' emotion regulation strategy, while others suggest that mindfulness should be described as a 'bottom-up' emotion regulation strategy. Current discrepancies might derive from the many different descriptions and applications of mindfulness. The present review aims to discuss current descriptions of mindfulness and the relationship existing between mindfulness practice and most commonly investigated emotion regulation strategies. Recent results from functional neuro-imaging studies investigating mindfulness training within the context of emotion regulation are presented. We suggest that mindfulness training is associated with 'top-down' emotion regulation in short-term practitioners and with 'bottom-up' emotion regulation in long-term practitioners. Limitations of current evidence and suggestions for future research on this topic are discussed.