Whisker and forelimb movements in rats have distinct behavioral functions that suggest differences in the neural connections of the brain regions that control their movements. To test this hypothesis, retrograde tracing methods were used to characterize the bilateral distribution of the cortical neurons that project to the whisker and forelimb regions in primary motor (MI) cortex. Tracer injections in each MI region revealed labeled neurons in more than a dozen cortical areas, but most labeling was concentrated in the sensorimotor areas. Cortical projections to the MI forepaw region originated primarily from the primary somatosensory (SI) cortex in the ipsilateral hemisphere. In contrast, most projections to the MI whisker region originated from the MI whisker region in the contralateral hemisphere. Tracer injections in the MI whisker region also revealed a higher proportion of labeled neurons in the claustrum and in the posterior parietal cortex. Injections of different tracers into the MI whisker and forepaw regions of some rats revealed a topographic organization of neuronal labeling in several sensorimotor regions. Collectively, these findings indicate that the MI whisker and forepaw regions receive different sets of cortical inputs. Whereas the MI whisker region is most strongly influenced by callosal projections, presumably to mediate bilateral coordination of the whiskers, the MI forepaw region is influenced mainly by ipsilateral SI inputs that convey somatosensory feedback.