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POP and IMAP are two protocols that mail programs use to access mail stored on remote computers.
How do I know if I normally use IMAP or POP to check my mail?
The vast majority of users access their mail using POP. So if you don't know which you use, you can safely assume it's POP.
What's the difference between IMAP and POP?
IMAP works by keeping mail on the server. POP works by downloading your mail to your computer.
What does this mean to me?
If you usually use POP to check mail, then when you use the Webmail interface you'll only have access to new mail -- none of your folders will be available. Likewise, if you create folders via Webmail and move mail to them, that mail will not be available the next time you check your mail via POP.
Also, IMAP will insert a message into your INBOX to keep track of certain things. This message will only be visible when you check your mail using POP. Despite what the message says, it is safe to delete it.
If you normally use IMAP to check your mail, then all of your folders will be accessible using the Webmail interface.
"POP" stands for "Post Office Protocol".
A POP account downloads mail to your local computer by default. Often, when a message is downloaded, it is deleted from the ISP's mail server. This prevents you from reading the same messages when you go to a different computer. Some mail clients, including Entourage, let you tell POP servers to leave mail on the server for a certain period of time. This allows you to read the same messages again from another computer, if necessary. You might want to do this if you read your mail from computers at work and at home, or on a desktop and a laptop computer. Even if you are using a single computer, it is a good idea to leave messages on the server for a day or two, in case you accidentally delete them from your local computer and wish to download a second copy.
The advantage of POP mail is that you have your messages with you and can peruse them even while you are not connected to the Internet, which is particularly desirable if you use telephone dial-up access to the Internet.
The disadvantage is that it is difficult to keep multiple computers synchronized. Messages you send from one computer are not copied on the other computers. You must either select one computer as your master computer, or you must download all the mail to each computer, which means more access time. If you intend to use a laptop computer while traveling, you may want to consider IMAP access.
"IMAP" stands for "Internet Message Access Protocol."
It is better than POP for accessing mail from multiple locations because it leaves the mail messages on the ISP's mail server. This lets you read the same messages regardless of what computer you use to read your e-mail. Messages you send are also stored on the mail server (if you keep copies, which is a good idea), so if you send a message from work, you will see that message when you access your mail from home or from a laptop while on the road. When you use an IMAP account you are, in fact, viewing your e-mail that is stored on the ISP's computer. There are no copies of the messages stored on your local computer unless you make a special effort to copy them there.
Because with IMAP your messages are kept on the ISP's computer indefinitely, some Internet providers do not support IMAP. It uses their disk storage space for your messages. Most ISP's set an upper limit on the amount of mail storage you can use, and the size may be too small for you if you get a lot of mail. For instance, five megabytes (5 MB) of storage may seem like a lot, but it can quickly fill up if you receive scores of messages every day, some with large attached files such as photos, which can often take a quarter megabyte for a single photo. A couple of rolls of family snapshots could fill your available storage. If that happens, messages addressed to you will be returned to the sender. Therefore, I recommend that you have at least 10 MB, and possibly more, for e-mail storage, if you plan to use IMAP, and that you closely monitor the space being used. If you cannot get adequate storage for IMAP, use a POP account and download your mail. Your choice of an Internet Provider may be determined in part by how much mail storage they allow you to have.
With IMAP, your mail remains on the server. Therefore, wherever you are and whatever computer you use, you always are looking at the same set of messages. Mail you read at work will show up marked as read when you view it from home. Replies you send while on the road will be there when you get home. The disadvantage, of course, is that you must have Internet access in order to view your mail at all, since it is never copied to your local computer.
Learn More: There is an excellent O'Reilly Article: Using IMAP on Mac OS X that explains the difference. The concept applies to using IMAP on OS 9.
This article helps you determine which one is right for you.