All taxpayers must make quarterly estimated tax payments to the Internal Revenue Service. For individual employees, this is done automatically through payroll tax withholding. Partners and S corporation shareholders must send in estimated payments on their own or face penalties and interest for underpayments.

Estimated Tax Requirements

You must make estimated tax payments if you expect to owe at least $1,000 in tax for the current year after subtracting any tax withholding or credits you will claim on your tax return. You must also pay if you expect the total of your withholding and credits to be less than 90 percent of your current year's taxes or 100 percent of the previous year's taxes -- whichever is smaller.

Project the Corporation's Income

If the company's income is consistent from month to month, you can use the average of the past few quarters as the basis for your estimated tax payments. S corporations with more volatile earnings should create a new estimate each month to make sure their estimated payments stay on track throughout the year. Look at past financial statements for historical trends that could help you project the company's future growth. Adjust for seasonal fluctuations, especially if you sell more products at the end of the year.

Salary Issues

You must take a salary if you perform work for the company, even if you are the sole shareholder. The IRS closely reviews salaries and owner distributions for S corporation shareholders. It can be easy for a company to abuse the income pass-through provisions and avoid paying payroll taxes. Your pay must be a reasonable salary for the type of work performed and the standard for the industry. The IRS can retroactively apply payroll taxes and any associated penalties and interest if it deems the salary too low. Calculate the federal and state tax withholding on your salary as well.

Personal Taxes

Because the corporation's income passes through, shareholders must also estimate the amount of their personal taxes for the year. Include your spouse's income and tax withholding amounts in these calculation if you are married. Total all of your estimated income items, such as salary, retirement plan distributions, interest, dividends and capital gains on investments. Add your share of the S corporation's income to find your total taxable income. Look up the taxes due from the tables in the previous year's instructions. Subtract any tax withholding taken out of your salaries. Divide the yearly tax by four to find the amount of your quarterly estimated tax payments. Use Form 1040-ES to report your payments to the IRS. Remember to also make any estimated state tax payments that are required in your area.