One of the many benefits of IRAs and other retirement accounts is that you can defer paying taxes on any capital gain. Whether you generate a short-term or long-term capital gain in your IRA, you don't have to pay any tax at all until you take the money out of the account. The negative is that all contributions and earnings you withdraw from an IRA, even profits from long-term capital gains, are treated as short-term capital gains and are taxable as ordinary income. You gain the benefit of tax-deferral but lose the benefit of the long-term capital gains tax rate.