Suggest you try the following: * Move all good emails out of the Inbox into other suitable folders. * Delete all emails you do not want. when Inbox is empty: * Empty the Deleted and Junk folder. * then compact all folders. - File > Compact folders. It is advisable that the Inbox should be used as an Inbox for incoming mail and not as a general store. As this folder gets a lot of activity you stand less chance of it becoming corrupted and losing emails. See info on maintaining a healthy Thunderbird. * http://kb.mozillazine.org/Keep_it_working_-_Thunderbird Usually, that message comes from the server. If this is a POP mail account, you can set up to auto delete messages that you delete. Tools > Account Settings > Server Settings for pop mail account you can choose to download and delete of server: * Do not select / uncheck 'Leave messages on server' Or * Select to 'Leave messages on server' then select what you want deleted: You can select both or either of these: * 'For at most xx days' (this will delete off server anything older than the xx days) * 'Until I delete them' - this will delete anything you manually delete. * click on OK