Neuroscientific evidence interprets both hypnotic trance induction and different meditation traditions as modified states of consciousness that emphasize attention, concentration and the letting go of thoughts, but they differ in terms of sensory input, processing, memory, and the sense of time. Furthermore, hypnosis is based on the suggestibility of a person and meditation on mindfulness; therefore it is not surprising to find differential brain plasticity changes. We analysed shared and non-shared neural substrates using electroencephalography (EEG), positron emission tomography (PET), and functional magnetic resonance imaging (fMRI). Most pronounced EEG changes were in deep as compared to light hypnosis (step-by-step induction) and in arm levitation where suggested movement was perceived as external. In a within-subject-design changes in brain activity during hypnosis and Tibetan Buddhist meditation were compared. High amplitudes in alpha frequency bands were most pronounced with meditation at frontal positions and with hypnosis in central and temporal locations. Significantly greater activity in theta 2 band was observed only with hypnosis in both hemispheres. PET cerebral activation patterns of imagery-mediated learning were analysed in hypnosis in a within-subject-design. Compared with baseline the learning of high-imagery words was associated with (i) more pronounced bilateral activation in the occipital cortex and prefrontal areas and (ii) improved memory performance. Visual illusion in hypnosis was studied with fMRI, analysed with Granger Causality Mapping, showing changes in the effective connectivity relations of fusiform gyrus, anterior cingulate cortex and intraparietal sulcus. Little is known about the neurobiological basis of the process of enhancing cognitive and emotional traits in meditation. In a longitudinal fMRI study attention abilities through intensive Soto-Zen meditation were investigated before (baseline), after training (6 months) and at follow-up (9 months). After six months differences were observed in the left inferior and left superior frontal gyrus; after 9 months activations in the left precuneus. Taken together, the findings advance understanding of the neural mechanisms that underlie hypnosis and meditation. Further studies with a greater sample size are needed to explore the differences and commonalities of hypnosis and different meditation techniques. Copyright © 2009 British Society of Experimental & Clinical Hypnosis. Published by John Wiley & Sons, Ltd.