You can register your copyright at any time during the existence of the copyright, but it's to your advantage to do it promptly. It is optimal to register the copyright within three months of first publication of the work.
If you register within three months of the publication of the work, you can get statutory damages and attorney's fees as well as actual damages and loss of profits. As I mentioned above, that can be a substantial difference.
If you register within five years of the publication of the work, the registration will establish "prima facie" evidence in court of the validity of the copyright. This seems to imply that after five years you're going to have to work a great deal harder to establish your rights, and certainly will limit what you can get for damages.
I suggest submitting your registration to the Copyright Office as soon as possible after first making your web site available on the Internet. If possible, submit your registration to the Copyright Office a few days before you plug the site in. Otherwise, do it soon after — but don't go over three months if you can help it.
Apart from some unusual circumstances to do with transferring and un-transferring the copyright, and even more obscure things, you never have to.
Note, however, that if you change the web site your registration doesn't cover the changes. You'll have to register the changes separately — optimally, every three months. I'll cover this later on. I only mention it here to indicate that changing the web site does not require the original copyright to be renewed.
Just think: if your site changes regularly and you conscientiously register the changes, you will have a fine collection of copyright certificates!
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