Yes,if you file jointly the IRS will offset your tax refund and apply it towards the back taxes owed. You could file Jointly
and also file Form 8379 Injured Spouse Allocation. Or you could file separately, but In most cases, you're
better off filing a joint return and including the injured spouse form.
There are a number of tax credits that are not available if filing
separately.
Also, if you live in
a community property state, joint items such as income actually need to be
split evenly between the two of you. Filing separate returns in a
community property state can add up to be a real headache, see IRS pub 555 if
this applies to you: http://www.irs.gov/uac/Publication-555,-Community-Property-1
If you file Form
8379 with your original return, it may take up to 11 weeks to process an
electronically-filed return or up to 14 weeks if you file a paper return. If you
file Form 8379 by itself after a joint return has been processed, then
processing will take about 8 weeks. To avoid delays, be sure to follow
the Form’s instructions.
See the following links to form 8379 and its instructions.
http://www.irs.gov/pub/irs-pdf/i8379.pdf
http://www.irs.gov/pub/irs-pdf/f8379.pdf
