Does a home encapsulation qualify for the energy-efficient improvement deduction?

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It depends, but it most likely will qualify. See the Instructions for Form 5695, line 19a:

"Enter the amounts you paid for any insulation material or system (including any vapor retarder or seal to limit infiltration) that is specifically and primarily designed to reduce the heat loss or gain of your home when installed in or on such home and meets the prescriptive criteria established by the IECC." (International Energy Conservation Code)

You would need to have certification from the manufacturer of the product to show that this was qualifying property.