Section 1244 of the Internal Revenue Code is the small business stock provision enacted to allow shareholders of domestic small business corporations to deduct a loss on the disposal of such stock as an ordinary loss rather than as a capital loss, which is limited to only $3,000 annually.
Normally, stock is treated as a capital asset, and if disposed of at a loss, the loss is deducted as a capital loss.
The general rule for net capital losses (losses that exceed gains in any tax year) is that they are subject to an annual deduction limit of only $3,000. Any excess loss over $3,000 must be carried forward to a future year (individuals may not carry back a capital loss to prior years).
On the other hand, a loss on Section 1244 stock is not subject to the annual $3,000 deduction limit. A loss on Section 1244 stock is deductible up to $50,000 ($100,000 on a joint return, even if only one spouse has a Section 1244 loss).
Claim a loss on section 1244 stock on Form 4797, and not Schedule D.