We have to pay someone who is in the U.S. on a J1 Visa, but has a SSN. Does she need to complete a W-8BEN or a W-9? Would she receive a 1099 or 1042-S? If a 1099, which one?

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You do not want a W-9 from this person, nor report on a 1099. As for which form you do want, it depends on what the payment is for—individual services? Or is it a scholarship or fellowship?  

If the payment is for services, you need a form 8233 from her (on which she may make a treaty claim to reduce or eliminate the 30% you must otherwise withhold), and you will report on the 1042-S. If payment is a scholarship or fellowship not in exchange for services, she should complete the W-8BEN (on which she can claim treaty benefits); reporting is still made on the 1042-S.

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