Judicial Transparency and Ethics Enhancement Act of 2006 - Amends the federal judicial code to establish the Office of Inspector General for the Judicial Branch of the U.S. government, to be headed by an Inspector General appointed by the Chief Justice.
Requires the Office to: (1) investigate matters pertaining to the Judicial Branch (other than the Supreme Court), including possible misconduct in office of justices and judges; (2) conduct and supervise audits and investigations; and (3) prevent and detect waste, fraud, and abuse.
Provides for whistleblower protection.