Homeless Veterans Assistance Act of 2006

Homeless Veterans Assistance Act of 2006 - Extends through: (1) FY2011 the homeless veterans comprehensive services program; (2) 2011 the authority of the Secretary of Veterans Affairs to provide treatment and rehabilitation for seriously mentally ill and homeless veterans; (3) 2011 the authority of the Secretary to transfer to homeless veterans' housing programs real property obtained by the Department of Veterans Affairs (VA) through foreclosure of home mortgages; (4) FY2011 a VA grant program for homeless veterans with special needs; (5) FY2011 the authorization of appropriations for the VA technical assistance grant program; and (6) FY2011 the Advisory Committee on Homeless Veterans.

Authorizes the Secretary to make emergency grants to entities providing care to homeless veterans for repairing or replacing facilities damaged or destroyed by a disaster.

Directs the Secretary to provide financial assistance to eligible entities to provide supportive services for very low income veteran families residing in permanent housing. Requires the equitable distribution of such assistance across geographic regions, including rural communities and tribal lands.

Requires the Secretary to carry out a demonstration program on preventing homelessness of veterans who are at risk of homelessness after they are discharged or released from active military service.

Makes permanent and extends to at least 12 (currently, six) locations a VA demonstration program of referral and counseling services for veterans transitioning from certain institutions (including penal and mental illness institutions) who are at-risk for homelessness.