The first three boxes separate interest by who gets to tax it. Box 1 is ordinary taxable interest: bank deposits, corporate bonds, accumulated dividends paid by a life insurance company, and interest on notes and debentures. Box 3 is interest on US savings bonds, Treasury bills, Treasury notes and Treasury bonds, and the instructions require that it be kept out of box 1. The reason is not cosmetic. Title 31 of the United States Code, section 3124(a), provides that "stocks and obligations of the United States Government are exempt from taxation by a State or political subdivision of a State," so box 3 interest is federally taxable and generally free of state and local income tax. Box 8 runs the other way: tax-exempt interest, chiefly from municipal bonds, is generally excluded from federal gross income and may or may not be taxable by your own state depending on who issued the bond.
Box 8 is reported precisely because it is not taxed. Tax-exempt interest appears on Form 1040 on its own line, and it is an input to several calculations built on top of adjusted gross income, most visibly the provisional income figure that decides how much of a Social Security benefit is taxable. Box 9 breaks out the portion of box 8 that came from specified private activity bonds, meaning private activity bonds issued after August 7, 1986, which is an alternative minimum tax preference item. The instructions are explicit that box 9 is included in the box 8 total, so the two are not added.
Box 2 is a deduction hiding inside an income form. It reports interest or principal forfeited because of an early withdrawal from a time deposit, typically a certificate of deposit cashed before maturity. The instructions are specific that the payer must not reduce box 1 by the forfeiture, so the form reports the full interest credited and the penalty separately. On the return the penalty is subtracted in arriving at adjusted gross income, under section 62(a)(9) of the tax code, which reaches amounts "forfeited to a bank, mutual savings bank, savings and loan association, building and loan association, cooperative bank or homestead association as a penalty for premature withdrawal of funds from a time savings account, certificate of deposit, or similar class of deposit." Because it is an above-the-line subtraction it is available whether or not you itemize.
Box 5 says what it is and the instructions say what it is not. Box 5 reports investment expenses for single-class real estate mortgage investment conduits, and the instructions carry a one-line note underneath: "This amount is not deductible." It is a residue of a deduction that no longer exists for individuals.
The bond adjustment boxes are for people who bought at other than par. Box 10 is accrued market discount, box 11 is bond premium on an ordinary taxable covered security, box 12 is bond premium on a Treasury obligation, and box 13 is bond premium on a tax-exempt bond. Each adjusts the interest a holder actually reports, and a payer that has already netted the adjustment into the interest figure leaves the box blank instead. Box 14 gives the CUSIP number of the bond, which is the only way to work out which state issued a tax-exempt bond, and therefore whether the interest is also exempt where you live.
Boxes 4, 6 and 7 are withholding and foreign tax. Box 4 is federal income tax withheld, which on this form means backup withholding applied because a taxpayer identification number was missing or flagged. Boxes 6 and 7 report foreign tax paid on interest and the country it went to, which is the input to a foreign tax credit or deduction.
Several things that feel like interest arrive on other forms. Interest that is taxable original issue discount goes on Form 1099-OID, and tax-exempt original issue discount goes in box 11 of that form. Dividends from money market funds go on Form 1099-DIV, not here, even though the economics look like interest. Exempt-interest dividends from a municipal bond fund also go on Form 1099-DIV, in box 12, which is why a direct bondholder and a fund holder receive the same economic income on two different forms.
The exempt recipient list is why some interest never generates a form. No Form 1099-INT is required for payments to a corporation, a tax-exempt organization, an individual retirement arrangement, an Archer medical savings account, a Medicare Advantage medical savings account, a health savings account, a US agency, a state, the District of Columbia, a US territory, or a registered securities or commodities dealer. Interest earned inside a retirement account falls under that list, which is the mechanical answer to why an IRA holding bonds produces no annual tax paperwork.