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 limited 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 limited 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 the Joint Committee on Taxation toidentify any limited tax benefits contained in any revenue or reconciliation measure amending the Internal Revenue Code that is being prepared for filing by a conference committee.
Makes it out of order to consider any measure containing an emergency designation if it also provides an appropriation or direct spending for any other item or contains any other matter. Allows the measure to contain rescissions of budget authority or reductions of direct spending, or reduce amounts for that emergency.
Provides for expedited judicial review of this Act.
Requires the President to submit legislation for the periodic review, reauthorization, and sunset of tax expenditures with his FY2008 budget.
Makes it out of order in the House to consider any measure containing a tax expenditure unless it terminates the tax expenditure within 10 years.