The advent of functional magnetic resonance imaging (fMRI) in non-human primates has facilitated comparison of the neurobiology of cognitive functions in humans and macaque monkeys, the most intensively studied animal model for higher brain functions. Most of these comparative studies have been performed in the visual system. The early visual areas V1, V2 and V3, as well as the motion area MT are conserved in humans. Beyond these areas, differences between human and monkey functional organization are increasingly evident. At the regional level, the monkey inferotemporal and intraparietal complexes appear to be conserved in humans, but there are profound functional differences in the intraparietal cortex suggesting that not all its constituent areas are homologous. In the long term, fMRI offers opportunities to compare the functional anatomy of a variety of cognitive functions in the two species.