Yes, large withdrawals before retirement age are subject to tax plus a 10% penalty. If you did not make estimated tax payments, you can also expect to be assessed a penalty for under-paying your taxes, even if you pay in full with your tax return.
There are a few exceptions to the 10% penalty, but the income is always subject to full income tax. There is a new exception to the penalty for a $1000 withdrawal for emergency expenses, and if you qualify as a "first time" home buyer, you can except another $10,000 from the penalty. (First time means you did not own the home where you lived for the two years prior to the new purchase.)
Otherwise, you pay the taxes and penalties.
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