A new system for organizing received messages for a user does not require the user to examine and categorize each received message, and enables the user to conveniently and efficiently modify filtering rules used to define folders that organize received messages. The system includes a received information database for storing received messages. One or more message filters are provided, for example where a separate message filter is provided to handle each specific message source or message type. Each message filter generates indices corresponding to portions of the received messages it processes. The message filters store the indices into a database index such that the indices are associated with the message and message portions to which they correspond. The system includes a plurality of message folders, such that received messages are organized based on a predetermined set of message characteristics. The system stores a search query within each folder. When the user requests to view the contents of a given folder, the search query for that folder is passed to a search engine. The search engine generates search results based on the search query and a search of the received message index. Messages are thus associated with the given folder, as defined by the search query, and appear to the user to be contained within that folder. In an example embodiment, the system includes an alert engine which periodically determines whether a message has been received that matches alert characteristics provided by the user.