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We're self-publishing a book in both paperback and e-book format. The content between the versions will be identical except for some formatting corrections (mainly white-space) made for the digital version.

We know that we need to have separate ISBN's for each version, but we are a little confused whether or not both versions need to be registered with the Copyright Office.

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Short answer: No. You are supposed to register only the "best edition" with the copyright office. They have a long list of criteria for what constitutes the best edition, but it's things like a hard cover takes precedence over a paperback. See http://www.copyright.gov/circs/circ07b.pdf

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Copyright applies the moment given work is solidified on a medium - the registration is not necessary at all providing that you have any reliable proof that you are the author. (you do have the copyright but the court is not omniscent, you need some way to show that you do.)

Registering with the Copyright Office only serves as such a proof, and a very solid one. Once it exists, there is no way for the other version with such minor differences to be someone else's work and not infringe on yours. It's a clear derivative, so a single registration is enough of a proof in any copyright cases - you have the claim to the original, so all derivative works either belong to you or infringe upon your rights, whichever is the case you win.

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