A system for collaborative document annotation whereby notes (i.e. annotations) associated with a document, such as an image or text document, are stored in a notes database on a central notes server. The documents and associated annotations are treated independently from each other whereby separate data structures are created for the documents and for the associated annotations. A web server application on the server side functions to capture requests from one or more note client applications for creating, storing, editing and retrieving annotations related to specific documents stored on the notes server. On the client side, the notes client functions to display the document that the user wishes to annotate and provides the tools necessary to permit the user to create, edit, delete, retrieve and store notes. A synchronization process transmits the annotations generated by the user from the notes client to the notes server. In response, the notes server transmits back an acknowledgement along with any new notes that other notes clients may have posted since the last synchronization was performed thus enabling multiple notes clients to annotate a document asynchronously with respect to each other. When annotations are posted to the notes server by a notes client, the state of the annotation database is synchronized such that all other notes clients can retrieve the current, up to date annotations associated with a document.