High Risk Terrorism Prevention Initiative of 2006

High Risk Terrorism Prevention Initiative of 2006 - Amends the USA PATRIOT Act to revise provisions regarding domestic preparedness grants to require the Secretary of Homeland Security (currently, the Office for Domestic Preparedness) to make such a grant each fiscal year to each state for a project that was eligible for a grant under the State Homeland Security Grants program or the Urban Area Security Initiative (UASI) made with amounts available for FY2006.

Permits the use of grants for UASI-eligible projects: (1) by a high threat, high density urban area to enhance state and local capabilitites to deter, prepare for, and respond to terrorist acts; (2) to purchase equipment, conduct exercises, and provide training and technical assistance to responders and to analyze intelligence information; (3) to construct, modify, or operate a facility in major metropolitan areas designated as a critical homeland security emergency operation node; and (4) for terrorist prevention and deterrence activities involving chemical, biological, radiological, or nuclear weapons. Authorizes the Secretary to allocate funds for UASI grants based on: (1) a quantitative assessment of the threats addressed, the vulnerability of persons and critical infrastructure to such threats, and the economic consequences if an attack occurs; and (2) the sustainability and effectiveness of grant activities. Sets forth provisions concerning grant priorities, municipality eligibility, and minimum allocation amounts.