The presence of primary cilia in corneal endothelial cells of a range of species from six non-mammalian vertebrate classes (Agnatha, Elasmobranchii, Amphibia, Teleostei, Reptilia and Aves) is examined by scanning and transmission electron microscopy. Our aim is to assess whether these non-motile cilia protruding into the anterior chamber of the eye are a consistent phylogenetic feature of the corneal endothelium and if a quantitative comparison of their morphology is able to shed any new light on their function. The length (0.42–3.80 μm) and width (0.12–0.44 μm) of the primary cilia varied but were closely allied with previous studies in mammals. However, interspecific differences such as the presence of a terminal swelling in the Teleostei and Amphibia suggest there are functional differences. Approximately one-third of the endothelial cells possess cilia but the extent of protrusion above the cell surface varies greatly, supporting a dynamic process of retraction and elongation. The absence of primary cilia in primitive vertebrates (Agnatha and Elasmobranchii) that possess other mechanisms to control corneal hydration suggests an osmoregulatory and/or chemosensory function.