Do not allow the Anti-Virus to fix/resolve anything. Anti-Virus products have no understanding that the Inbox mbox file contains more than just one email. If you let Anti-Virus fix things you risk losing everything in the Inbox. It's possible the email arrived in Inbox and was marked as junk which then displayed email in Junk. It's also possible that since then you have emptied the Junk, so in effect you cannot see the email in question. Therefore, it's possible that Anti-Virus is picking up 'marked as deleted' and 'hidden' residual data still lurking in the mbox files. Background info to help explain situation: When you delete or move and email, that email get 'marked as deleted' and 'hidden', but in reality is still in the relevant mbox file. So when you or Thunderbird decided that email in 'Inbox' was 'Junk', it got moved to Junk folder. The original email in Inbox' is still in Inbox but it is 'marked as deleted' and 'hidden'. When you emptied/deleted emails from junk, the original email in 'Junk' is still in Junk but it is 'marked as deleted' and 'hidden'. Or maybe it was two separate emails and one went to Junk and the other went to Inbox, but maybe subsequently both have been deleted by you hence why you cannot see those emails. That explains why the Anti-Virus says bad email in pop account Inbox and bad email in pop account Junk. What should you do assuming you have deleted those emails: * Right click on 'Inbox' and select 'Compact folder' * Right click on 'Junk' and select 'Compact folder' Compacting means eg: Inbox file is opened and Thunderbird scans through it looking for all your good and wanted emails which it copies to a new file. Meaning all those 'marked as deleted' emails get ignored. Then the original file is deleted and the new file replaces it. Then the 'hidden' traces of a bad email will be completely erased. Compacting folders is basically good housekeeping. It removes old traces of previously moved or deleted email, reduces the size of the mbox file and keeping file in a healthy state reduces the risk of corruption. More info on compacting (do not confuse this with compression aka zipped they are not the same): * https://support.mozilla.org/en-US/kb/compacting-folders '''re :What is difference between Inbox and Inbox.msf and junk vs junk.msf''' The 'Inbox' and 'Junk' files are mbox text files and they contain downloaded emails. The 'Inbox.msf' and 'Junk.msf' files are index files used by Thunderbird. Basically, the Message List is data got from the index file and when you select an email, Thunderbird uses that data to locate the stored email in the relevant mbox file, so it can display contents in the Message Pane.