As far as I know, you need to compare the messages on the server, with your database of messages that you have already read. Many POP clients use an optional "UIDL" header for this purpose, using these UIDL's as the key for their database of what messages have been read.

You might also use an optional "Status" header, which some POP clients also use. If a message does not have these headers on it, you'll have to add them yourself, and you'll have to change the content of this header yourself too, as far as I know (and then save the modified message back to the server again).

Looking quickly in the jguru JavaMail tutorial in a discussion on message "flags" it says that they are not supported under POP3, and "Checking for new mail is not a POP task but one built into mail clients."...