Reading from javamail takes a long time

It would always be messages[i].getContent() that would be the slowest part of the code. The reason is normally IMAP server would not cache this part of message data. Nevertheless, you can try this:

    FetchProfile fp = new FetchProfile();
        fp.add(FetchProfile.Item.ENVELOPE);
        fp.add(FetchProfileItem.FLAGS);
        fp.add(FetchProfileItem.CONTENT_INFO);
    fp.add("X-mailer");

and after you have specified the fetch profile then you do your search/fetch of messages. 

Basically the concept is that the IMAP provider fetches the data for a message from the server only when necessary. (The javax.mail.FetchProfile is used to optimize this). The header and body structure information, once fetched, is always cached within the Message object. However, the content of a bodypart is not cached. So each time the content is requested by the client (either using getContent() or using getInputStream()), a new FETCH request is issued to the server. The reason for this is that the content of a message could be potentially large, and if we cache this content for a large number of messages, there is the possibility that the system may run out of memory soon since the garbage collector cannot free the referenced objects. Clients should be aware of this and must hold on to the retrieved content themselves if needed.

By using the above mentioned code snippet you could 'hope' for some speed improvement but it solely depends on your SMTP server if this would work or not. All the big SMTP server do not support this behaviour because of the load issue mentioned in the previous paragraph and hence you may not gain any speed.

I finally solved this issue and wanted to share.

The solution, at least the one that worked to me, was found in this site: http://www.oracle.com/technetwork/java/faq-135477.html#imapserverbug

So, my original code typed in my first post becomes to this:

Session sesion = Session.getInstance(System.getProperties());
Store store = sesion.getStore("imap");
store.connect(host, user, passwd);
Folder inbox = store.getFolder("INBOX");
inbox.open(Folder.READ_WRITE);

// Convert to MimeMessage after search 
MimeMessage[] messages = (MimeMessage[]) carpetaInbox.search(new FlagTerm(new Flags(Flags.Flag.SEEN), false));
for (int i = 0 ; i< messages.length ; i++){
    // Create a new message using MimeMessage copy constructor
    MimeMessage cmsg = new MimeMessage(messages[i]);
    // Use this message to read its contents 
    Object obj = cmsg.getContent(); 
// ....
}

The trick is, using MimeMessage() copy constructor, create a new MimeMessage and read its contents instead of original message. You should note that such object is not really connected to server, so any changes you make on it, like setting flags, won't take effect. Any change on message, have to be done on original message.

To sum up: This solution works reading large Plain Text mails (up to 15Mb) connecting to an Exchange Server using IMAP protocol. The times lowered from 51-55min to read a 13Mb mail, to 9seconds to read same mail. Unbelievable.

Hope this helps someone and sorry for English mistakes ;)