Corticothalamic fibres, which originate from layer VI pyramidal neurons in the cerebral cortex, provide excitatory synaptic inputs to both thalamic relay neurons and reticular neurons; reticular neurons in turn supply inhibitory inputs to thalamic relay neurons. Pyramidal cells in layer VI in the mouse somatosensory cortex highly express mRNA encoding kainate receptors, which facilitate or depress transmitter release at several synapses in the central nervous system. We report here that contrary modulation of transmitter release from corticothalamic fibres onto thalamic relay and reticular neurons is mediated by activation of kainate receptors in mouse thalamic ventrobasal complex and thalamic reticular nucleus. Exogenous kainate presynaptically depresses the synaptic transmission at corticothalamic synapses onto thalamic relay neurons, but facilitates it at corticothalamic synapses onto reticular neurons. Meanwhile, the lemniscal synaptic transmission, which sends primary somatosensory inputs to relay neurons, is not affected by kainate. In addition, GluR5-containing kainate receptors are involved in the depression of corticothalamic synaptic transmission onto relay neurons, but not onto reticular neurons. Furthermore, synaptically activated kainate receptors mimic these effects; high-frequency stimulation of corticothalamic fibres depresses synaptic transmission onto relay neurons, but facilitates it onto reticular neurons. Our results suggest that the opposite sensitivity of kainate receptors at the two corticothalamic synapses is governed by cortical activity and regulates the balance of excitatory and inhibitory inputs to thalamic relay neurons and therefore their excitability.