Hi,

I am resident alien for the tax purpose(4+ years on h1b). My wife had her OPT status in 2009 and got 1099 from her employer.

If we file together(married filed jointly) as alien resident, do we need to pay SE Tax(social security) on her income?

Thanks.

Normally if your wife had W-2 income on OPT and you both choose to file joint return, you do not pay SS tax and Medicare tax.
But I am not sure if same treatment applies to 1099-misc income as on OPT you normally get W-2.

From page 51 of IRS publication 519.
"Self employment income you receive while you are a resident alien is subject to self-employment tax even if it was paid for services you performed as a nonresident alien."

Services were performed while she was nonresident alien. She received payment while she was nonresident alien. So, it should not be subject to SE tax. Resident status was changed later on.