Pop mail accounts must be set up to 'leave messages on the server'. check this before using. * Tools > Account Settings > Server Settings for the mail account or * menu icon > Options > Account Settings > Server Settings for the mail account select: 'leave messages on the server' optional: select: 'for at most xx days' this will delete anything older than specified number of days select 'Until I delete them' when you delete an email it will be deleted off the server. click on Ok to save settings. Pop mail accounts only look at Inbox and download whatever has not been previously downloaded regardless of whether it has been read or not. They cannot access nor download from any other folder on the server. If you wanted to download emails in other fodlers, you would have to move emails into the Inbox in order to download them and this may not be very practical in your situation. What you can do is synchronize your IMAP folders to get a copy downloaded to your IMAP mail account. Then go into 'offline' mode to stop any further synchronizing as synchronized folders do get updated. MozBackup tool could now be used to backup the Profile as synchronising created mbox files which contain emails. You can also do the following to get a copy outside of the IMAP mail account: Create the same folders in 'Local Folders'. Then right click on email and 'copy to' and select Local Folders and the folder you require. Putting a copy in Local Folders means these emails are also on your computer and they are not influenced by anything you do in the IMAP folders. You would need to backup emails in these folders. See info: * http://kb.mozillazine.org/IMAP_backup MozBackup: * http://mozbackup.jasnapaka.com/ ImportExporttool: * https://addons.mozilla.org/en-US/thunderbird/addon/importexporttools/