In order to investigate the existence of anatomical subdivisions within the thalamic reticular nucleus (Rt), the distribution of reticular neurons expressing the calcium binding protein calretinin was investigated in the rat by means of immunocytochemistry. Calretinin immunoreactive (Cr-ir) neurons were mainly distributed in the lateral and ventral regions, and along the medial border of the Rt rostral pole. Caudal to the rostral pole, many neurons were Cr-ir in the more dorsal part of the rostral two-thirds (the "dorsal cap") of the Rt. Fewer Cr-ir neurons were present more caudally along the lateral and medial borders, and in the caudalmost part of the nucleus, related to the acoustic thalamus. The distribution of Cr-ir neurons in the rostral Rt was compared with that of neurons projecting to the ipsilateral and contralateral anterior, intralaminar, midline, and mediodorsal nuclei, or to the contralateral rostral Rt. The retrograde transport of Fluorogold revealed a remarkably precise topography of the rostral Rt: different reticular areas were found to project to different thalamic nuclei, or to different rostrocaudal or mediolateral portions of the same thalamic nucleus, with a limited degree of overlap. The double-labeling experiments demonstrated that the reticular neurons projecting to the ipsilateral anterodorsal, midline, mediodorsal, and anterior intralaminar nuclei frequently expressed calretinin; by contrast, the majority of the reticular commissural neurons did not express the protein, with the exception of neurons projecting to the contralateral mediodorsal and midline nuclei. The ipsilaterally projecting calretinin-positive neurons were frequently located along the medial edge of the rostral pole and in the dorsal cap of the nucleus, segregated from the commissural calretinin-negative neurons. The combined analysis of calretinin expression patterns and tract tracing data provided further insight in the anatomical organization of the thalamic reticular nucleus, suggesting a different neurophysiological role for the ipsilaterally vs. the contralaterally projecting reticular neurons in the modulation of the synaptic activity of the dorsal thalamus.