I came to US in 4/2010 as a Physician in Training on H1b (india). I filed 2010 Taxes as a Resident alien. I transferred from H1b to J1 in 7/2011 due to program requirement. Now Filing taxes for 2011, I was h1b for 6 months and J1 physician for 6 months. My country has tax treaty with US, So I am applicable to avail this treaty and file for tax refund based on J1 since it is valid for 2 years. I was wondering if any one can advice regarding tax filing for my case, I am confused if I have to file as Resident alien (H1b)for first 6 months and as non resident alien(J1) for last 6 months of 2011.
Thanks

First, you filed incorrectly for 2010. You filed as a resident alien, while you SHOULD have filed as a dual-status alien. If you were married and filed JOINTLY for 2010, then the return is accurate PROVIDED you reported all world-wide income for 2010.

For 2011, you are mis-interpreting the tax treaty. The two-year exemption for which you THINK the J-1 visa applies ONLY IF you are a teacher, visiting scholar or researcher. Based on your post, you are a TRAINEE, which means your J-1 status applies for 2011 and 2012 ffor tax purposes. You MUST pay taxes under a trainee J-1 visa, but your ARE exempt from FICA (Social Security and Medicare) taxes for 2011 while under the J-1 visa and for all of 2012.

For 2011, you need to file a dual-status return AGAIN, with Form 1040NR being the controlling documemt, with Form 8843 to report your J-1 status.

For 2012, you will file as a non-resident alien, filing Form 1040NR and 8843.

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Thanks a lot for your kind input, I appreciate. I filed 2010 return Married Jointly, as a Resident Alien.
Here is some information I found " J1 - Student attending a college or university, usually as a graduate student.
Trainee of some type, either for a foreign business who sent him here to receive specialized training with a U.S.-based corporation, or as an individual undergoing some type of post-college training. Resident physicians and law interns fall into this category."
I am a Physician undergoing my training here in US. Will This makes me eligible to take Advantage of US-India Tax treaty (exempt from taxes for 2 years)?
As I understand correctly, For all the period I am on J1 - I do not pay FICA taxes.
Thanks

You are exempt from FICA while under the J-1 visa for 2011 and 2012, but you are NOT exempt from income taxes as a J-1 trainee.

For 2011 you can file joint as residents, but for 2012, you MUST file as a non-resident alien.

MAKE SURE your FICA exemption was implemented for 2011 BEFORE you file the joint return because you will not be able to request a FICA tax after the joint return is filed.

Thanks for your kind reply.
I had one more query, I had my wife (not employed) and 1 yr old son with me during entire 2011. Both were dependent on me. Being a J 1 physician in training from India, I was wondering how can I claim for my wife and son?
Thanks a lot

Yes, you CAN claim your wife and child as dependent on your non-resident return, because you are considered to be a TRAINEE under your J-1 visa.

If you want my professional help, double-click on my title above and scroll down to my profile/signature. You will find my email address and websites there.