The primary goal of this study was to identify the collateral projection from the dorsal raphe (DR) nucleus to whisker-related, trigeminal sensory and facial motor systems in the rat. Following the injections of two retrograde tracers, gold-conjugated and inactivated wheatgerm agglutinin-horseradish peroxidase (WGA-apo-HRP-gold) and Fluorogold (FG) within vibrissae-related, sensory and motor areas at the cerebral cortical, thalamic, and medullary levels, the distribution of double-labeled neurons was examined within each subdivision of the DR. The major findings were: 1) the 5-HT-immunoreactive, DR neurons projecting to vibrissae-related, primary sensory and motor cortices were mainly observed in the ventromedial subdivision, with a few cells in the dorsomedial subdivision; 2) the DR neurons projecting to ventroposteromedial and ventrolateral thalamic nuclei were observed in the lateral wing subdivision ipsilateral to the injection sites; and 3) the DR neurons projecting to vibrissae-related, principal trigeminal and facial motor nuclei were also located mainly in the lateral wing subdivision ipsilateral to the injection sites. Taken together, these observations provide evidence that midline vs. lateral wing DR subdivisions have a differential functional organization with respect to their efferent projection systems and that individual DR neurons in each subdivision might preferentially send axon collaterals to sensory and motor whisker system targets, thus providing an anatomical substrate for coordination of whisker movement and tactile sensory coding.