The murine olfactory system is composed by two main functional units, the vomeronasal organ (VNO) and the main olfactory epithelium (MOE). Sensory neurons in the VNO are characterized by the expression of two families of pheromone receptors, vomeronasal type-1 receptors (V1Rs) and vomeronasal type-2 receptors (V2Rs). The functional interplay between the VNO and the MOE in sexual and reproductive behaviours is nowadays well accepted, with both structures able to detect overlapping sets of volatile and non-volatile molecules, but the receptorial systems and the sensory cells involved in pheromone detection by the MOE are unknown. Moving from a custom microarray profiling olfactory microvillar cells and from an unprecedented high-throughput genomic analysis of the whole MOE transcriptome, here we describe for the first time the expression of vomeronasal receptors in the MOE. We recently developed NanoCAGE and we applied it to the MOE; analysis of data revealed the expression of multiple V1Rs and V2Rs from discrete clusters, and this was confirmed by RT-PCR. We demonstrated by double-label fluorescent in situ hybridization that selected members of the V1R and V2R families are expressed in both olfactory sensory neurons and microvillar cells, which recently have been hypothesized to be a new sensory cell type in the MOE. Our results provide a fundamental molecular basis to the lately accumulating evidences of the MOE and the VNO as highly functionally integrated structures.