In functional studies of the human brain using functional magnetic resonance imaging (fMRI) we often observe some functional areas that are commonly activated by different stimulus inputs even when the inputs are of different categories. It is difficult to distinguish by fMRI whether the neuronal circuits activated for processing these inputs are separate and independent ones within the functional area or whether they are mutually interactive and possibly sharing a part of the circuits for processing some common features of the input information. In order to elucidate such property of the neuronal circuits, we used a novel paradigm in which paired input stimuli with varied inter stimulus interval (ISI) were presented during a stimulation period in fMRI experiments. The refractory suppression induced by an input pair depends on ISI as well as the differing characteristics of the input pair. The extent of suppression, an indicator for the interaction between the processing activities of the input pair, can be evaluated by the shape of the time-course of fMRI responses. We examined the functional characteristics of the neuronal circuits in areas that were activated by different inputs of inter-category types, namely face stimuli and building stimuli and also by intra-category input pairs such as different faces. In the ventral visual occipitotemporal region, we found functional areas where neuronal circuits were interacting to process these inputs rather than functioning as separate independent circuits. With this approach, one can probe functional system activity at the neuronal circuit level to learn the characteristics that determine the functional roles of certain brain areas.