The thalamic reticular nucleus (TRN), receiving excitatory inputs from thalamic nuclei and cortical areas, regulates thalamic sensory processing through its inhibitory projections to thalamic nuclei. Higher cognitive function has been shown to affect this regulation from the prefrontal cortex (PFC). The present study examined how activation of the PFC modulates auditory or visual responses of single TRN cells in anesthetized rats, using juxta-cellular recording and labelling techniques. Electrical microstimulation of the medial PFC did not evoke cell activities in the TRN, but it altered sensory responses in the majority of auditory (40/43) and visual cells (19/20) with regard to response magnitude, latency and/or burst spiking. Alterations in response magnitude were bidirectional, either facilitation or attenuation, including induction of de novo cell activity and nullification of sensory response. Response modulation was observed in early (onset) and/or recurrent late responses. PFC stimulation, either before or after early response, affected late response. Alterations occurred in the two types of cells projecting to the first- and higher-order thalamic nuclei. Further, auditory cells projecting to the somatosensory thalamic nuclei were affected. Facilitation was induced at relatively high incidences as compared with that in the sub-threshold intra- or cross-modal sensory interplay in the TRN where attenuation is predominated in bidirectional modulation. Highly complex cooperative and/or competitive interactions between the top-down influence from the PFC and bottom-up sensory inputs are assumed to take place in the TRN to adjust attention and perception depending on the weights of external sensory signals and internal demands of higher cognitive function.