A method and system for synchronizing a main database of a server and a local database of a handheld device. A user can use an application residing in the handheld device to make transactions in the local database. In a synchronization operation, a synchronization client is used to: establish a connection between a server and the synchronization client; receive an identifier for the main database's structure from the server; receive an identifier for the version of the handheld application from the server; send transaction information to the server; receive metadata to update the handheld application; and receive data extracted from the main database from the server. The synchronization client is also used to update filter information used by the server to reduce the size of the data downloaded to the handheld device.