The mouse prefrontal cortex (PFC) is an umbrella term for rostrally located neocortical brain regions. The anterior cingulate, pre- and infralimbic, orbital, agranular insular and secondary motor cortices are generally included in the PFC. The PFC is critically involved in the acquisition and expression of flexible behavioral responses to changing sensory information, and prefrontal signalling to (neocortical) sensory regions is assumed to be essential to these processes.In the present study, we characterized the anatomical organization of excitatory, prefrontal projections to neocortical sensory (i.e. somatosensory, auditory, visual) regions using retrograde viral tracing in transgenic mouse lines identifying three main classes of pyramidal neurons (i.e. layer 2/3 IT, layer 5 IT, layer 5 IT/PT). As part of this work, we developed an open-source software platform (DMC-BrainMap) for analysis of (whole-brain) anatomical data.Our results reveal profound differences in the organization of PFC projections to the sensory cortices. Only the visual and auditory cortices receive predominant input from the orbital subregions of the PFC. Interestingly, we found a dorsoventral gradient of the different classes of pyramidal neurons projecting to both cortices, respectively. In contrast, the somatosensory cortices predominantly receive input from the secondary motor cortices (irrespective of PFC pyramidal class). Additionally, the somatosensory cortices receive moderate input from the orbital and agranular insular cortices displaying stark differences between pyramidal cell classes.In conclusion, our results provide further insights into the anatomical organization of sensory-prefrontal circuits opening the possibility for its functional interrogation by future research.