First of all - you are confident that these messages are still on the server? Are you using POP or IMAP in Thunderbird? If you want to see your email from several devices, then IMAP is the best choice on all of your devices. And if you have IMAP and are seeing some messages but not others in any particular folder, then I'm going to be stumped. With POP, an email client has to keep track of what it has downloaded. Thunderbird uses a file named popstate.dat for this, but if it has never downloaded the missing messages, this shouldn't be relevant. But you could look for popstate.dat in your profile and delete (or better, move or rename) it. https://support.mozilla.org/en-US/kb/profiles-tb The remaining possibility that comes to mind is that the server considers your message has been read so thinks it doesn't need to serve it to you again. Does marking messages as unread in the webpage or iPhone make them visible in Thunderbird?