Thalamocortical connections are a neuroanatomical feature shared among vertebrates, although the extent and organization of these connections vary among species. From an evolutionary standpoint, reptiles represent early stages of the pattern of connectivity between the thalamus and cortex, and elucidation of these pathways may help to reveal the biological significance of these projections. The present tract tracing study was performed to examine the organization of thalamocortical projections in the pond turtle, Pseudemys scripta elegans. All experiments were carried out using in vitro brain preparations. Injections of neurobiotin into the medial cortex resulted in labeled neurons in the ipsilateral dorsomedial anterior nucleus of the thalamus, those in the dorsomedial cortex labeled neurons in the dorsolateral anterior nucleus, and injections into the dorsal cortex resulted in labeled neurons in the dorsal lateral geniculate nucleus of the thalamus. Injections of neurobiotin into these thalamic nuclei confirmed the projections to the cortex. Finally, neurobiotin injections primarily into the medial cortex resulted in bilateral label of axons and terminals in the suprapeduncular nucleus of the hypothalamus. The results of the neurobiotin injections revealed a topographic pattern of thalamocortical connections such that medial cortical regions connect with medial thalamic nuclei and lateral cortical regions connect with lateral nuclei. These findings suggest that the presence of functionally segregated thalamocortical projections is a conserved feature of brain organization among amniotes. Moreover, this work describes a descending pathway linking cortical regions with the red nucleus via the hypothalamus thereby providing indirect cortical control of the reptilian rubrospinal system.