Recently, Yohe and Krell (The Anatomical Record, vol. 306:2765–2780) lamented the incongruence between genetics and morphology in the vomeronasal system of bats. Here, we studied 105 bat species from 19 families using histology, iodine‐enhanced computed tomography (CT), and/or micro‐CT. We focused on structural elements that support a functional peripheral vomeronasal receptor organ (vomeronasal organ [VNO]), together comprising the “vomeronasal complex.” Our results support prior studies that describe a functional VNO in most phyllostomid bats, miniopterids, and some mormoopids (most known Pteronotus spp.). All of these species (or congeners, at least) have vomeronasal nerves connecting the VNO with the brain and some intact genes related to a functional VNO. However, some bats have VNOs that lack a neuroepithelium and yet still possess elements that aid VNO function, such as a “capsular” morphology of the vomeronasal cartilages (VNCs), and even large venous sinuses, which together facilitate a vasomotor pump mechanism that can draw fluid into the VNO. We also show that ostensibly functionless VNOs of some bats are developmentally associated with ganglionic masses, perhaps involved in endocrine pathways. Finally, we demonstrate that the capsular VNC articulates with the premaxilla or maxilla, and that these bones bear visible grooves denoting the location of the VNC. Since these paraseptal grooves are absent in bats that have simpler (bar‐shaped or curved) VNCs, this trait could be useful in fossil studies. Variable retention of some but not all “functional” elements of the vomeronasal complex suggests diverse mechanisms of VNO loss among some bat lineages.