To investigate the somatotopic organization of the cerebellum, we analysed multisynaptic inputs to the primary motor cortex (MI) using retrograde transneuronal transport of rabies virus. At 3 days after rabies injections into proximal forelimb, distal forelimb and hindlimb representations of the macaque MI, second-order neurons via the thalamus were labeled in the deep cerebellar nuclei, including the dentate (DN), anterior interpositus (AIN) and posterior interpositus nuclei. In the DN, the labeling of both the forelimb and hindlimb was seen mainly in the dorsal aspect. The labeling of the hindlimb was located rostral to that of the forelimb and the labeling of the proximal forelimb was located slightly rostral to that of the distal forelimb. The same rostrocaudal arrangement was observed in the AIN. In the posterior interpositus nucleus, however, labeling from the MI hindlimb and forelimb representations largely overlapped. At the 4-day postinjection period, third-order labeling occurred in Purkinje cells of the cerebellar hemisphere. The Purkinje cell labeling from the forelimb representation, including the proximal and distal regions, was observed primarily in lobules IV–VI and crus I. The proximal forelimb labeling was both rostral and lateral to that of the distal forelimb within lobules IV–VI. However, the hindlimb labeling was seen both rostral and lateral to that of the proximal forelimb within lobules III–VI. These results indicate that the hindlimb, proximal forelimb and distal forelimb are arranged rostrocaudally in the DN and AIN, whereas there is dual somatotopy along the rostrocaudal and lateromedial axes in the cerebellar cortex.