The dorsal raphe (DR) is invested with nitric oxide synthase (NOS)-expressing profiles. To characterize the connections of NO-containing cells and further assess neurochemical relationships maintained by DR, the transmitter identity of the raphe projection to the trigeminal somatosensory system was examined. Rats were injected with retrograde tracer into vibrissae-related target areas or with anterograde tracer into DR. NADPH-diaphorase (NADPHd) histochemistry or NOS-immunostaining was combined with serotonin (5HT)- or serotonin transporter (SERT)-immunolabeling to examine: 1) the presence of NO in 5HT-containing axons from DR; 2) the distribution of NO-containing fibers with respect to other nitrergic profiles in the somatosensory system; and 3) the propensity for individual projection neurons in specific subdivisions of DR to colocalize 5HT and NO. Results confirm that “barrel-like” patches can be identified in several adult trigeminal relay nuclei by NADPHd histochemistry and demonstrate that fibers from DR contain 5HT and NO. Observations include a high percentage of cortical midline projection neurons which contained NADPHd (70–80%) and coexpressed 5HT. In contrast, ∼40% of retrogradely labeled DR-thalamus cells in the lateral wing demonstrated NADPHd or 5HT expression, but not both in the same neuron. Colocalization of NADPHd and 5HT within individual DR projection neurons indicates that: i) DR is a source of nitrergic input to trigeminal structures, and ii) NO and 5HT may be simultaneously released to influence information-processing within somatosensory targets. Disparities in NADPHd expression between retrogradely labeled DR neuronal subpopulations further suggest functional differences in the impact of NO on cortical and subcortical targets. J. Comp. Neurol. 466:495–512, 2003. © 2003 Wiley-Liss, Inc.