Zero Tolerance for Veterans Homelessness Act of 2009

Zero Tolerance for Veterans Homelessness Act of 2009 - Directs the Secretary of Veterans Affairs (VA) to establish a program within the Veterans Benefits Administration (VBA) for the prevention of veteran homelessness by identifying veterans who are homeless or at imminent risk of becoming homeless and providing assistance, including short and medium term rental assistance and housing relocation and stabilization services, to ensure that such veterans do not become or remain homeless.

Makes VBA regional offices responsible for oversight and coordination of: (1) any housing programs for veterans supported by the Department of Housing and Urban Development (HUD); and (2) the program described above.

Includes new construction projects as projects under which eligible entities may receive grants for furnishing certain services to homeless veterans. Requires the study of the payment method for the reimbursement of grant recipients for per diem payments for furnishing services to homeless veterans and the development of an improved method to reimburse grant recipients for services furnished to homeless veterans.

Amends the United States Housing Act of 1937 to set forth requirements for public housing agencies to provide vouchers for rental assistance to veterans (under current law, on behalf of homeless veterans with chronic mental illnesses or chronic substance use disorders) through the HUD-VA supported housing program.

Establishes in HUD a Special Assistant for Veterans Affairs in the Office of the Secretary.

Requires: (1) establishment of a method for the annual collection and aggregation of data on homeless veterans who participate in VA-HUD programs; and (2) submission to Congress of a comprehensive plan for ending homelessness among veterans.