A method and system that allows efficient shredding of large instances of hierarchical data structures into relational data structures. Large instances of hierarchical data structures, which are able to be larger than the random access storage of a computer used to shred them into relational data structures, are incrementally shredded into a temporary storage. When the amount of data shredded into the temporary storage reaches or exceeds a predetermined commit count, the data in the temporary storage is transferred to a relational data structure maintained by a relational database manager. A Document Type Description annotation is provided to allow the end user to specify execution order for SQL commands and to specify commit count values.