New Homestead Act of 2006

New Homestead Act of 2006 - Directs the Secretary of Education to repay a specified percentage (up to $2,000 per year) of certain education loans to an individual who completes a degree and both resides and is employed for at least five years in an area outside a metropolitan statistical area which for 20 years has a net out-migration of inhabitants of at least 10% of the county population (qualifying county).

Amends the Internal Revenue Code to allow a: (1) tax credit for the lesser of $5,000 or 10% of the purchase price of a principal residence in a qualifying county; and (2) capital loss deduction with respect to a sale or exchange of a principal residence in a qualifying county.

Provides for the creation of tax-exempt individual homestead accounts, funded by individual cash contributions and matching Federal contributions according to a specified formula, whose tax-free distributions after five years are used by residents of qualifying counties for qualified higher education or medical expenses, first-time homebuyer or business capitalization costs, or rollovers.

Establishes a rural investment tax credit of 70% of the present value of new buildings (including rehabilitation projects) or 30% of the present value of existing buildings.

Establishes a qualified rural small business investment credit of 30% of expenditures for starting or expanding a business, including costs for capital, plant and equipment, inventory expenses, and wages, but not including interest costs.

Provides for accelerated depreciation of business property in rural investment projects.

New Homestead Venture Capital Fund Act - Amends the Consolidated Farm and Rural Development Act to establish the New Homestead Venture Capital Fund (Fund), owned by private investors, to generate and provide equity capital to rural businesses in qualifying counties. Directs the Secretary of Agriculture to provide funding and guarantees for private investors in the Fund.