Objectives: Our previous study showed that long-term practitioners of Sahaja Yoga Meditation (SYM) had around 7% larger grey matter volume (GMV) in the whole brain compared with healthy controls; however, when testing individual regions, only 5 small brain areas were statistically different between groups. Under the hypothesis that those results were statistically conservative, with the same dataset, we investigated in more detail the regional differences in GMV associated with the practice of SYM, with a different statistical approach. Design: Twenty-three experienced practitioners of SYM and 23 healthy non-meditators matched on age, gender and education level, were scanned using structural Magnetic Resonance Imaging. Their GMV were extracted and compared using Voxel-Based Morphometry. Using a novel ad-hoc GLM model, statistical comparisons were made to observe if the GMV differences between meditators and controls were statistically significant. Results: In the 16 lobe area subdivisions, GMV was statistically significantly different in 4 out of 16 areas: Right hemispheric temporal and frontal lobes, left frontal lobe and brainstem. In the 116 AAL area subdivisions, GMV difference was statistically significant in 11 areas. The GMV differences were statistically more significant in right hemispheric brain areas. Conclusions: The study shows that long-term practice of SYM is associated with larger GMV overall, and with significant differences mainly in temporal and frontal areas of the right hemisphere and the brainstem. These neuroplastic changes may reflect emotional and attentional control mechanisms developed with SYM. On the other hand, our statistical ad-hoc method shows that there were more brain areas with statistical significance compared to the traditional methodology which we think is susceptible to conservative Type II errors.