Emails are downloaded and written one after the other in the order they were downloaded to a single text file. When you delete an email from eg: 'Inbox', it is 'marked as deleted' and hidden from view. But, it is not removed from the 'Inbox' file just in case you want to recover it. When you compact the 'Inbox', the 'marked as deleted' email is removed. This recovers space and tidies the Inbox file. The most common folders that have a load of 'marked as deleted' emails tend to be 'Inbox', 'Drafts' and 'Junk'. So these folders would need regular compacting. If a file eg: 'Inbox', is previously corrupted by perhaps an Anti-Virus product or a lack of compacting or another reason, then when you compact that corrupted file, the markers may not be detectable and this can lead to loss of emails in that 'Inbox' file. If a folder has only stored emails and not had any emails deleted from it then it will not need compacting. There are no 'marked as deleted' emails in it. Compacting is not to be confused with compressing, they are entirely different. Good info here: http://kb.mozillazine.org/Thunderbird_:_Tips_:_Compacting_Folders Are you talking about a pop or imap mail account? If imap, do you know if you actually download the entire email or just the headers - are the folders synchronised for offline use ?