The paraventricular nucleus of the thalamus (PVT) is part of a group of midline and intralaminar thalamic nuclei implicated in arousal and attention. Recent research points to anatomical and functional differences between the anterior (aPVT) and posterior PVT (pPVT). The present study re-examines the main sources of brain inputs to the aPVT and pPVT in the rat following iontophoretic injections of the retrograde tracer cholera toxin B (CTb) in the PVT. The location and the number of retrogradely labeled neurons in different regions of the brain were examined to determine which brain areas are likely to exert a strong influence on the aPVT and pPVT. The largest number of labeled neurons was found in layer 6 of the prelimbic, infralimbic and posterior insular cortices following injections in the pPVT. In contrast, the largest number of labeled neurons following injections of CTb in the aPVT was found to be in the hippocampal subiculum and the prelimbic cortex. Other areas of the brain including the reticular nucleus of the thalamus, periaqueductal gray, parabrachial nucleus and dorsomedial nucleus of the hypothalamus were found to contain a more moderate number of neurons following injections of CTb in either the aPVT or pPVT. The results of the present tracing study clearly show that more neurons in the prefrontal cortex and subiculum project to the PVT than neurons from the hypothalamus and brainstem. These results highlight the potential importance of top-down modulation of PVT mechanisms and behavioral functions.