The calretinin-positive (CR+) neurons of the paraventricular thalamic nucleus (PVT) have been recognized to play pivotal role in modulating stress and arousal states. In the accompanying poster (Kota et al.), we defined several brain regions containing glutamatergic, GABAergic or mixed populations of neurons that project to PVT. In this study, we mapped cortical and subcortical afferents in the PVT and examined their distribution relative to the PVT/CR+ neuron population. We used vGLUT2-Cre, vGAT-Cre, and vGLUT2-Cre/vGAT-Flp double transgenic mouse strains to explore subcortical inputs via anterograde viral tracing, and employed Rbp4-Cre, FoxP2-Cre, and NTSR1-Cre strains to label layer-specific cortical inputs. We validated the synaptic connections with electron microscopy.With the exception of thalamic reticular nucleus (TRN) that innervated both CR+ and CR- regions in PVT, all other subcortical afferents displayed significant selectivity to the “core”, CR+ region of the PVT. Subcortical inputs arising from distinct brain regions or from the same brain regions with distinct transmitter phenotype converged in the CR+ zone of PVT. In contrast, cortical inputs from layer 5 pyramidal cells selectively targeted the lateral, “shell” zone of the PVT. Layer 6 inputs labelled in FOXP2 animals entered both the core and the shell region.Our data show that the major top-down and bottom-up afferents that have strong impact on PVT activity are segregated. Our data defines a central “core”” region which integrates multiple subcortical excitatory and inhibitory afferents and a peripheral “shell” region that is under cortical layer 5 influence.