I file taxes as a Resident Alien, which makes my tax situation pretty much identical to most American PhD students at Columbia. And yet, because of legal liability, the only qualified people who are willing to give us advice are tax professionals (whose time will cost at least $100
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EDIT: Indeed, your link claims they are obligated to report it on form W-2.
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If your stipend is taxable, Columbia fucked up big-time by not withholding. Check with them. Normally you pay federal income tax only on the portion of your stipend that isn't going to pay for university tuition and fees -- but you get a W-2 for it.
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I believe when I paid taxes on this situation, I filled out the tuition and 1098 on the correct form and did the math (which comes to 0*).
*OK it came out to like $100 for me because the scholarship didn't cover some fees or something.
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