This article assumes that you are using QuickBooks (desktop) and QuickBooks Enhanced Payroll. QuickBooks Payroll allows for two different methods by which you can track Medical Health Premiums for S-Corp Officers. You may have been processing S-Corp Health Insurance premiums using a Scorp Pd Med Premium Payroll Item all year long, but many S-Corps will choose to simply apply the S-Corp Health Insurance premiums they have been paying to an officer’s payroll at year end. This article discusses the method for making these year-end payroll adjustments......
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Editor's note and Disclosure:
While we believe, based upon a review of the applicable provisions by our consulting tax advisor, the controlling provisions of the tax code in this situation are:

Exception for S corporation shareholders. Do not treat a 2% shareholder of an S corporation as an employee of the corporation for this purpose. A 2% shareholder is someone who directly or indirectly owns (at any time during the year) more than 2% of the corporation's stock or stock with more than 2% of the voting power. Treat a 2% shareholder as you would a partner in a partnership for fringe benefit purposes, but do not treat the benefit as a reduction in distributions to the 2% shareholder.
S corporation shareholders. Because you cannot treat a 2% shareholder of an S corporation as an employee for this exclusion, you must include the value of accident or health benefits you provide to the employee in the employee's wages subject to federal income tax withholding. However, you can exclude the value of these benefits (other than payments for specific injuries or illnesses) from the employee's wages subject to social security, Medicare, and FUTA taxes.
This article is presented for information purposes only. If you are unsure how the item discussed in this article should affect tax forms or taxability; you should consult with your own accountant and/or tax advisor for assistance.