Mindfulness meditation has beneficial effects on brain and body, yet the impact of Vipassana, a type of mindfulness meditation, on heart rate variability (HRV) - a psychophysiological marker of mental and physical health - is unknown. We hypothesised increases in measures of well-being and HRV, and decreases in ill-being after training in Vipassana compared to before (time effects), during the meditation task compared to resting baseline (task effects), and a time by task interaction with more pronounced differences between tasks after Vipassana training. HRV (5-minute resting baseline vs. 5-minute meditation) was collected from 36 participants before and after they completed a 10-day intensive Vipassana retreat. Changes in three frequency-domain measures of HRV were analysed using 2 (Time; pre- vs. post-Vipassana)x 2 (Task; resting baseline vs. meditation) within subjects ANOVA. These measures were: normalised high-frequency power (HF n.u.), a widely used biomarker of parasympathetic activity; log-transformed high frequency power (ln HF), a measure of RSA and required to interpret normalised HF; and Traube-Hering-Mayer waves (THM), a component of the low frequency spectrum linked to baroreflex outflow. As expected, participants showed significantly increased well-being, and decreased ill-being. ln HF increased overall during meditation compared to resting baseline, while there was a time *task interaction for THM. Further testing revealed that pre-Vipassana only ln HF increased during meditation (vs. resting baseline), consistent with a change in respiration. Post-Vipassana, the meditation task increased HF n.u. and decreased THM compared to resting baseline, suggesting post-Vipassana task-related changes are characterised by a decrease in absolute LF power, not parasympathetic-mediated increases in HF power. Such baroreflex changes are classically associated with attentional load, and our results are interpreted in light of the concept of \'flow\' - a state of positive and full immersion in an activity. These results are also consistent with changes in normalised HRV reported in other meditation studies.