The VO Registry provides a mechanism with which VO applications can discover and select resources that are relevant for a particular scientific problem. This specification defines the operation of this system. It is based on a general, distributed model composed of searchable and publishing registries, as introduced at the beginning of this document. The main body of the specification has three components: (a) an interface for harvesting publishing registries, which builds upon the Open Archives Initiative Protocol for Metadata Harvesting. (b) A VOResource extension for registering registry services and description of a central list of said IVOA registry services. (c) A discussion of the Registry of Registries as the root component of data discovery in the VO.