Employing a retrograde fluorescent double labeling technique, we compared the localization of subthalamic nucleus (STN) cells projecting to the striatum and nucleus tegmenti pedunculopontinus pars compacta (TPC), with that of STN cells sending axon collaterals to both the globus pallidus and substantia nigra in the rat. The STN-striatal projections were mostly the third branches of massive STN-pallidal and STN-nigral collateral projection neurons, whereas only very rarely did the STN-TPC projections contribute to these collateral projections. The TPC projecting STN cells, giving rise to an independent output of the nucleus, were located mainly in its thin lateral strip region. The STN may integrate the somatic motor information from various cortical/subcortical brain areas (including the motor cortex, striatum, globus pallidus, thalamus and TPC), and disperse it predominantly to the pallidal complex, substantia nigra and striatum by way of axon collaterals, and to a lesser degree to the TPC through separate fibers. Thus, the STN might be in a strategic position to exert a prominent control over the basal ganglia-related somatic motor functions.