The Additional Medicare Tax is an additional (0.9%) tax to wages, compensation, and self-employment income, if an individual's income exceeds the threshold amount for their individual filing status. This is a new tax added by the creation of the Affordable Care Act (ACA). For more information, please use the IRS Questions and Answers for the Additional Medicare Tax link.
This tax is calculated on Federal Form 8959 Additional Medicare Tax and that form also reconciles the amount of tax owed against what an employer has already withheld from an employee's paycheck (and so is included as withholding in Box 6 of Form W-2 Wage and Tax Statement along with the regular Medicare tax withholding).
The threshold for calculating the additional tax is $250,000 for those filing with a status of Married Filing Joint ($125,000 for those filing with a status of Married Filing Separate and $200,000 for those filing with a status of Single, Head of Household, or Qualifying Widow(er)).
The calculation of the additional tax can be a bit confusing because IRS Form 8959 does not actually "net" the difference between what your employer withheld and what the tax is in your situation, but transfers both amounts to Federal Form 1040 U.S. Individual Income Tax Return. Adding to the confusion, are the instructions from the IRS to employers to calculate the amount to withhold from their employees’ pay using the threshold of $200,000. They do this as the employers cannot be certain what filing status their employees will ultimately use on their tax return.
The IRS created Form 8959 to reconcile the amount actually owed against the amount deducted by the employer. If you print your return (and the form is applicable in your situation), you will see this form as part of the return. In Part I, they use the appropriate threshold amount for your filing status to calculate the additional tax on Line 7. This amount is then transferred to Line 18 of the form and from there to Line 8 of Schedule 2 (Form 1040) Additional Taxes to add to your total tax due. Part V of the form calculates the additional amount your employer already withheld from your pay and that amount appears on Line 24 and from there goes to Line 15 of Federal Form 1040 to add to your total tax withheld. In this way, the two amounts net out to reconcile what your actual additional tax is against the amount your employer withheld and included on your Form W-2.
Federal Form 8960 Net Investment Income Tax—Individuals, Estates, and Trusts was also introduced in 2013. If this form is applicable to your return, it will also print with the return. This form calculates the additional tax on net investment income (if applicable in your situation).
Note that any link in the information above is updated each year automatically and will take you to the most recent version of the document at the time it is accessed.