Although the rat medial agranular cortex (AGm) has been implicated in a variety of motor functions, the source of the afferents impinging upon thalamic neurons projecting to the AGm is not directly known. The main purpose of this study was to determine whether the AGm is a major recipient of the nigrothalamocortical pathway. This issue was addressed by two sets of experiments. First, the organization of the nigrothalamic projections was studied by light and electron microscopy following injections of the anterograde tracer Phaseolus vulgaris-leucoagglutinin (PHA-L) into the pars reticulata of the substantia nigra (SNR). The major finding of this study was the disclosure of a heretofore unknown projection to the rostromedial part of the ventral anterior-ventral lateral complex (VAL). This projection originates exclusively from the ventral portion of the SNR and is comparable in strength to the well-known nigrothalamic projection to the ventromedial nucleus (VM). Electron microscopic examination revealed differences in the synaptic organization of nigral terminals in the VAL and the VM. A large proportion of the labeled terminals in the VAL was involved in axosomatic synapses, whereas, in the VM, the axosomatic synapses were rare, and 67% of nigral terminals were found in contact with thin dendrites. To assess a possible disynaptic nigrothalamocortical pathway to the AGm, a double-labeling strategy combining PHA-L injections in the SNR and pressure injections of the retrograde tracer, cholera toxin subunit B (CTB) in the AGm was employed. The greatest density of CTB-labeled neurons was found in the rostral and central portion of the VAL, coincident with the nigrothalamic labeling originating from the ventral SNR. Electron microscopic analysis confirmed that some of the PHA-L-labeled terminals established synaptic contacts with the CTB-labeled cell bodies and large dendrites. In conclusion, our findings indicate that there exist two different nigrothalamocortical pathways through the motor thalamus in the rat. The SNR-VAL-AGm cortical projection may play a role in oculomotor functions, whereas the SNR-VM-cortical pathway has been implicated in arousal mechanisms.