Witness Security and Protection Act of 2006 - Amends the federal judicial code to establish in the U.S. Marshals Service a Short Term State Witness Protection Program to provide protection for witnesses in state and local trials involving homicide or other major violent crimes pursuant to cooperative agreements with state and local criminal prosecutor's offices and the U.S. attorney for the District of Columbia.

Authorizes the Attorney General to make grants to eligible prosecutor's offices for the purpose of providing short term protection to witnesses in trials involving homicide or serious violent felony.