Separate Enrollment and Line Item Veto Act of 2006

Separate Enrollment and Line Item Veto Act of 2006 - Prohibits the congressional appropriations committees from reporting any appropriations measure that fails to contain the same level of detail on the allocation of a proposed item of appropriations set forth in the accompanying committee report.

Prohibits any congressional committee from reporting an authorization measure that contains new direct spending or a new targeted tax benefit unless it presents each as a separate item, and the accompanying committee report contains a level of detail clearly indentifying its allocation.

Prohibits a conference committee from filing a conference report that fails to contain the level of detail and the separate itemization of each direct spending or targeted tax benefit required by this Act.

Makes it out of order in the House to consider any measure reported or presented in violation of this Act.

Provides for separate enrollment of each item of every appropriation and authorization measure containing new direct spending or new targeted tax benefits passed by Congress in the same form.

Requires amounts of budget authority, new direct spending, and revenues represented by a new targeted tax benefit contained in an Act that is vetoed (and not overridden by Congress) to be dedicated only to deficit reduction, and not to be used as an offset for other spending increases.

Requires adjustments to congressional committee allocations resulting from such a veto.

Provides for expedited judicial review of this Act.