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I am a PhD student in the US, originally from Germany and here on a F-1 visa.

Mid last year, my status changed from being on a fellowship to being on a research assistantship. Hence, I got a 1042-S and a W-2. I have been using the tax treaty so far and would like to continue declaring taxes for my US income in Germany.

However, the tax return generated with the GLACIER Tax Prep (formerly CINTAX) software says that the tax treaty can only be applied to the fellowship (1042-S):

http://i.stack.imgur.com/kHVfy.png

Is this true? If not, what information could I have entered that made it think that the tax treaty does not apply?

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From the treaty:

Subject to the provisions of Articles 16 (Directors’ Fees), 17 (Artistes and Athletes), 18 (Pensions, Annuities, Alimony, and Child Support), 19 (Government Service; Social Security), and 20 (Visiting Professors and Teachers; Students and Trainees), salaries, wages, and other similar remuneration derived by a resident of a Contracting State in respect of an employment shall be taxable only in that State, unless the employment is exercised in the other Contracting State.

Looks like you're out of luck on this. You have to pay the US taxes.

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