Background Obstruction of endolymph flow by saccular otoconia has been linked to endolymphatic hydrops and is a key pathological hypothesis for Ménière’s disease. The inner ear hosts several macrophage populations. Endolymphatic sac macrophages can phagocytose otoconia, and spiral limbus macrophages express genes for fluid shear stress sensing and bone remodelling. Since macrophages are strongly affected by in-flammatory status, a role for them in otolith removal could provide a link between in-flammation and hydrops. However, no data are available so far about macrophages around reuniting and endolymphatic duct, the two thin structures where blockage is most likely to happen. Methods We performed tissue clearing and lightsheet imaging on rat temporal bones. Autofluorescence and immunolabeling for collagen IV, SMA and Iba1 were used to identify and quantify inner ear structures, blood vessels and macrophages. Results The connective tissue layer underlying the reuniting duct branched from the cochlear spiral limbus and was connected to it through its microvascular network. Reuniting duct and spiral limbus hosted a continuous macrophage population, con-taining both ameboid and branched cells. Macrophages also surrounded the underly-ing vestibulocochlear artery. A separate macrophage population, similar to that found in the saccular connective tissue, was found around the endolymphatic sinus and utriculo-endolymphatic valve; macrophage features changed pattern in the vestibular aqueduct and again at the endolymphatic sac. Conclusion Macrophages appear localized at strategical positions for the sensing of endolymphatic and perilymphatic pressure, and for the removal of clogging material, such as otolith aggregates, from reuniting and endolymphatic ducts.