Kilon (kindred of IgLON) and opioid-binding cell adhesion molecule belong to the IgLON subgroup of immunoglobulin superfamily together with the limbic system-associated membrane protein and neurotrimin. In the present study, we have analyzed biochemical and ultrastructural characterization of Kilon and opioid-binding cell adhesion molecule such as regional and developmental expression patterns, light and electron microscopic localization, and intermolecular interactions. Western blotting revealed a widespread distribution pattern of Kilon with high expression levels in the olfactory bulb, cerebral cortex, diencephalon, hippocampus, and cerebellum and low expression levels in the medulla oblongata and spinal cord. In contrast, opioid-binding cell adhesion molecule showed a regionally restricted expression pattern with high levels only in the cerebral cortex and hippocampus. Expression of Kilon and opioid-binding cell adhesion molecule was increased gradually during postnatal development and maintained until adulthood. Light microscopic immunohistochemistry demonstrated that the localization of opioid-binding cell adhesion molecule and Kilon coincided well with that of vesicle-associated membrane protein 2, a synaptic marker protein, in the cerebral cortex and hippocampus of adult brain. In the cerebellum, Kilon-immunoreactive puncta were observed to colocalize well with that of vesicle-associated membrane protein 2, while opioid-binding cell adhesion molecule immunoreactivity was observed only at part of synaptic glomeruli in the granular layer and rare in the molecular layer. Electron microscopic analysis revealed that Kilon and opioid-binding cell adhesion molecule immunoreactivity was observed mainly at postsynaptic sites of dendritic and somatic synapses in adult cerebral cortex and hippocampus. Only trace levels of Kilon and opioid-binding cell adhesion molecule were detected in the soluble fraction of a cortical homogenate, although a substantial amount of F3 was present in the soluble fraction. A binding analysis using a cross-linker and the immunoprecipitation technique demonstrated that Kilon and opioid-binding cell adhesion molecule interacted heterophilically and homophilically. These findings show that Kilon and opioid-binding cell adhesion molecule are clearly distinguishable from each other in regional expression and localization, and binding patterns. These differences possibly represent diverse functions of each IgLON molecule.