l-Afadin was originally purified from rat brain as an actin filament (F-actin)-binding protein that was homologous to the AF-6 gene product. Concomitantly, s-afadin that did not show an F-actin-binding capability was copurified with l-afadin. Structurally, s-afadin lacks the C-terminal F-actin-binding domain but has two short sequences that were not present in l-afadin. The properties and roles of l-afadin have intensively been investigated, but those of s-afadin have poorly been understood. We show here an additional difference in their biochemical properties other than binding to F-actin between l-afadin and s-afadin. Both l-afadin and s-afadin bound to nectins, immunoglobulin-like cell adhesion molecules, whereas s-afadin more preferentially bound to nectins than l-afadin. The PDZ domain of l-afadin and s-afadin was essential for their binding to nectin-3. The dilute domain of l-afadin negatively regulated its binding to nectin-3, but the deletion of the C-terminal F-actin-binding domain of l-afadin did not increase the binding of l-afadin to nectin-3. These results indicate that the s-afadin-specific C-terminal inserts may be involved in its preference of binding to nectin-3 and raise the possibility that there are proteins other than nectins that more preferentially bind s-afadin than l-afadin.