The human suprachiasmatic nucleus (SCN), the master biological clock, is a small (∼2 mm3) and deep structure located in the anterior hypothalamus. Previous methods do not allow in vivo study of the human SCN in a non-invasive manner. Therefore, we explored blood oxygen level-dependent (BOLD)-functional magnetic resonance imaging (fMRI) with OFF–ON–OFF block-designed visual stimuli to record the activities in the ‘SCN and peri SCN in the anterior hypothalamus’ (SCN+) and the primary visual area V1 using a 3T Siemens scanner and six normal subjects. We found that: (i) the BOLD-fMRI response to light and the mean of percentage activation in the SCN+ at midday was significantly less than that at night; and (ii) the number of activated voxels in most of the visual area V1 at midday was significantly higher than that at night. We conclude that BOLD-fMRI responses to light in the SCN+ and the V1 areas vary with time of day. This conclusion is consistent with: (i) the previously measured phase–response curve to light [J. Physiol., 549.3 (2003) 945] for the SCN activity at critical intensity threshold; and (ii) the interaction of the melanopsin-based signals with the rod-cone signals at the ‘giant’ retinal ganglion cells [Nature, 433 (2005) 749] for the V1 activity.