Cinematographic stimuli have been previously used to probe functional mapping of naturalistic stimuli, leaving whether such stimuli are also associated with a subjective increase of the sense of presence (SoP). In this functional magnetic resonance imaging, we investigated whether the SoP evaluation of 3D-surround cinematographic stimuli was associated with any change of activity within emotion-related areas, in particular the amygdala. The subjects evaluated several scenes of a commercial 3D movie presented in four different conditions: 3D vision with surround sounds (3D-Surround), 2D-Surround, 3D-Mono, and 2D-Mono. The behavioral results showed that the stereoscopic viewing, but not surround sound, increased SoP scores. The wholebrain imaging results showed that the middle occipital gyrus was involved in evaluating the SoP. The planned anatomical ROI analysis showed that also activity in the right amygdala increased with increasing SoP scores. The results suggest that 3D vision enhances the SoP and this is associated with activation of both visual cortex and emotion-related brain region.