While interest on municipal bonds is tax free for federal income tax purposes, gain or loss on the sale of the bonds must be reported. The loss is treated as a capital loss, which is deductible within capital loss rules. That is, the loss can fully offset gains. Then, up to $3,000 of losses can be used to offset ordinary income ($1,500 for those who are married filing separately). Any excess capital loss can be carried forward to the following year.
The difference between amount realized and adjusted basis on the sale or exchange of capital assets. Long-term capital gains are taxed favorably. Capital losses are deducted first against capital gains, and then again up to $3,000 of other income.