Email messages stored on a mail server are filtered to identify the email messages that contain unwanted content. The mail server receives incoming email messages over a network. A content filter performs an initial scan to identify the incoming email messages that contain unwanted content by determining whether signatures associated with the email messages are included on a list of signatures that identify email messages that are known to include unwanted content. The email messages that are not identified as containing unwanted content are forwarded to appropriate mail boxes on the mail server. Multiple scanning threads perform a subsequent scan of the email messages in the mail boxes to identify those email messages containing unwanted content that were not identified by the initial scan. The subsequent scan determines whether signatures associated with the email messages in the mail boxes are included in an updated list of the signatures.