Is there a penalty for filing separately if married, if you've filed joint in the past?

There is no special direct penalty.  However, the Married Filing Separately filing status does not allow the taxpayer certain deductions and credits that might be available to other filing statuses.  MFS is by far the WORST filing status in the tax laws under most circumstances.

It is uncommon that MFS is a better choice than MFJ. Many of the people who believe they are better off MFS think that because they are not preparing their returns properly.

The "Married Filing Separately" filing status carries higher tax rates than the “Married Filing Jointly” filing status.  Also, many deductions and credits that are available to MFJ filers are not available to MFS filers. Three well-known such items that are not available to MFS filers are the Earned Income Credit,  the Child and Dependent Care Credit and any of the education deduction/credits (American Opportunity, Lifetime Learning, Tuition and Fees Deduction).

Additionally, if one spouse itemizes deductions, the other spouse must also itemize deductions and is precluded from using the standard deduction.

People usually use MFS when they can't agree to file jointly. Occasionally, the right combination of situations will create a smaller total tax than on a joint return, such as when one spouse has significant medical expenses, but it's rare.

About the only advantage to filing separately is that one spouse is not responsible for what's on the other's return (including the tax).

Regarding that last comment, you can still use the MFJ filing status and include a Form 8379 Injured Spouse Claim with your return.  This protects any refund of one spouse in a joint return from being used to satisfy the debts and/or obligations of the other spouse.  The Form 8379 is included within TurboTax under Federal Taxes, Other.

I am told that married persons filing tax returns in Ohio may be able to benefit from filing their Federal returns separately to significantly reduce their state tax obligations.  Ohio filers should take this into consideration in evaluating the above comments.