This study analyzed the projections of the basilar pontine nuclei (BPN) and of the nucleus reticularis tegmenti pontis (NRTP) to the two sides of the cerebellum in the rat. It showed that the two sides of the cerebellar cortex were innervated by different percentages of BPN (about 82% of the cells project to the contralateral cortex and 18% to the ipsilateral) and NRTP cells (some 60% project to the contralateral cortex and 40% to the ipsilateral). In comparison to projections traced to the cortex, only a few fibers were traced to the nuclei of the same animals. Most of the projections of the BPN to the cerebellar nuclei were traced to the lateralis and posterior interpositus nucleus of the contralateral side (95%), while a few were traced to homologous nuclei of the ipsilateral side (5%). Thus, the BPN principally control the activity of the contralateral cerebellum, with a much less important control over the activity of the ipsilateral cerebellum. Vice versa, the NRTP, which project to the lateralis, interpositus, and medialis nuclei of the two sides, with percentages (64% contra- and 36% ipsilateral) similar to those reported for the projections to the cortex, is more concerned in the bilateral control of the cerebellum, although with a moderate contralateral prevalence. The fact that projections of the BPN were principally traced to the contralateral nuclei, from which the efferent projection fibers from the cerebellum originate, suggests that the BPN are principally involved in the motor control of the contralateral body. Conversely, the bilateral projections of the NRTP to the cerebellar nuclei suggest that the NRTP is mainly involved in bilateral motor activities. The comparison of the projections to the cortex and nuclei of the cerebellum of single animals supports the co-existence of coupled (i.e., projections to the cortex and the corresponding nuclei) and uncoupled (i.e., projections to the cortex but not to the nuclei) projection patterns, from both the BPN and the NRTP. These features of the pontocerebellar projections open new vistas on the functional architecture of this pathway.