The suprachiasmatic nucleus (SCN) projections to the midline and intralaminar thalamic nuclei were examined in the rat. Stereotaxic injections of the retrograde tracer cholera toxin-β subunit (CTb) were made in 12 different thalamic sites. These included individual midline thalamic nuclei (anterior, middle, and posterior portions of the paraventricular thalamic nucleus (PVT), intermediodorsal, paratenial, rhomboid, or reuniens nuclei) and intralaminar thalamic nuclei (lateral parafascicular, central lateral, or central medial nuclei) as well as the mediodorsal and anteroventral thalamic nuclei. After 10–14 days survival, the brains from these animals were processed histochemically and the distribution of retrogradely-labeled neurons was mapped throughout the rostralcaudal extent of the SCN. Within this collective group of midline and intralaminar thalamic nuclei, the only region innervated by the SCN was the PVT. Approximately 80% of this projection arose from the dorsomedial SCN, and the remaining projection originated from the ventrolateral SCN which targeted mainly the anterior division of the PVT. Virtually no SCN neurons were labeled after CTb injections centered in any of the other midline thalamic nuclei, which includes the intermediodorsal, mediodorsal, paratenial, rhomboid, or reuniens thalamic nuclei. Similarly, no evidence for a SCN projection to the intralaminar thalamic nuclei was found. The discussion focuses on the role of SCN → PVT pathway in modulating cerebral cortical functions.