Your business structure determines what federal taxes you must pay and how you pay them. Some of the taxes require payment throughout the year, so it’s important to know your tax obligations before the end of your tax year. There are five general types of business taxes: Income tax Self-employment tax Estimated tax Employer tax Excise tax Each category of business tax might have special rules, qualifications, or IRS forms you need to file. If your business has employees, you might be required to withhold taxes from their paychecks. Federal employment taxes include income, Social Security and Medicare, unemployment, and self-employment taxes.