Eph receptors and their ligands, termed ephrins, have been implicated in axon guidance, neuron–target interactions, regional compartmentalization, and synaptic functions in nervous systems. These activities of the Eph family molecules prompted us to investigate whether these molecules play roles in the maintenance, regeneration and plasticity in the mature peripheral vestibular system. Using reverse transcription-polymerase chain reaction (RT-PCR), Western blot and immunocytochemical analyses, we identified distinct and reciprocal expression patterns of full-length isoforms of EphA5, EphA6, EphA7, EphB1, ephrin-A2 and ephrin-B1 that correlated with structural features of the peripheral vestibular system in adult rats. All of the Eph receptors and ephrins examined were localized in the cell bodies of vestibular ganglion neurons in vivo and in vitro, and were readily detected in their outgrowing neurites in vitro. In the utricle, these molecules were localized in distinct cellular and subcellular compartments corresponding to discrete features of utricular afferent innervation, e.g. defasciculation, branching and synapse formation. Taken together, these results identify the Eph receptors and ephrins as candidate molecular substrates for defining some aspects of the structural organization of the adult peripheral vestibular system.