The present invention is directed to a pluggable custom data binding system and method utilizing a generic data structure exchanged between a run-time system and a user define binding logic in Web Service Applications. The custom data binding system may replace the existing mappings for XML schema types. The custom binder is a function that works with the pairing of a particular XML schema type and Java type. The custom binder may define an interface including serialize and de-serialize methods to convert between Java objects and SOAPElements. After the custom binder is plugged into the run-time system, this custom binder may interact with the run-time system through use of SOAPElement. The custom binding provider may aggregate related custom binders to support particular custom data bindings. The custom binding provider may be created for a specific application that has a few XML schema types that are not supported by the JAX-RPC specification.