The IRS keeps track of income you receive from employers, brokerage houses and financial intuitions. Their computer system matches information they receive from these sources to your tax return.
If the IRS thinks you did not report all of your income, they will send you a letter asking for an explanation. Included in this letter is a calculation of how much additional tax they think you owe.
Sometimes these letters are not as bad as they seem. You may have legitimate deductions to offset the increased income. In many cases the IRS will actually wind up owing you additional refunds and interest.