The structural organization of the thalamic reticular nucleus was investigated by injecting the fluorescent dye, Lucifer yellow, intracellularly into identified neurons in fixed of tissue slices of the rat brain. This method provides a complete picture of the dendritic geometry of reticular nucleus neurons and is particularly useful for exploring the microcircuitry of selected regions of the brain, since it can be used in conjunction with other neuroanatomical techniques. Having successfully established the facilities for this work, the structure of individual neurons in the thalamic reticular nucleus has been carefully examined and documented. The afferent input to the thalamic reticular nucleus has than been studied using both anterograde and retrograde axonal fiber tracing techniques. In addition to the well known inputs from collaterals of principal neurons in the thalamus and corticothalamic neurons in layer VI of the cerebral cortex, the general region of the reticular nucleus also receives inputs from several cholinergic cell groups. These include the parabrachial nucleus, the pedunculopontine nucleus, and the magnocellular nucleus basalis. Anterograde tracer injections into the parabrachial nucleus or the pedunculopontine nucleus label axonal arbors within the closely adjacent zona incerta, but do not label those within the reticular nucleus. In contrast, tracer injections into the nucleus basalis result in a significant amount of diffusely organized and widespread axonal terminal arbors within the thalamic reticular nucleus. These findings suggest that the thalamic reticular nucleus may be pivotal in the cholinergic modulation of inputs to the cerebral cortex.