I had the same problem and tried several different methods to fix it, but all failed. This problem seems to only plague my Thunderbird connection to my MSN account. What I found that did work, most of the time (still get the odd duplication) is to set that email account to "not" leave the message on the email server. Here is how: # Right Click the Email Account, in the submenu click "settings". # Click "Server Settings" in the left column under the email account # Right panel, uncheck "leave messages on server". That will grey out the days selector and the "until I delete them" option. # Click "OK". Then go into your webmail for your webmail account (like MSN, or GMail, etc) or into your webmail access for your website and delete the emails from the inbox and trash. Clean it out. This should hopefully resolve it. For any other email accounts you setup in Thunderbird that are connected to any other mail server, do the same.