Legislative Line Item Veto Act of 2006

Legislative Line Item Veto Act of 2006 - (Sec. 2) Amends the Congressional Budget and Impoundment Control Act of 1974 to authorize the President to propose the cancellation (line item veto) of any dollar amount of discretionary budget authority, item of direct spending, or targeted tax benefit within 45 days after its enactment.

Sets forth requirements for the President's transmittal to Congress of a special message regarding a proposed cancellation. Prohibits duplicate proposals of such cancellations. Limits such messages to five for most bills or joint resolutions, but up to 10 for any omnibus budget reconciliation or appropriation measure.

Dedicates any cancellation only to deficit reduction or increase of a surplus.

Requires: (1) the chairs of the Senate and House Budget Committees to revise committee allocations and aggregates and other appropriate levels under the appropriate concurrent resolution on the budget to reflect the cancellation; and (2) the Office of Management and Budget (OMB) to revise applicable limits, as appropriate, under the Balanced Budget and Emergency Deficit Control Act of 1985 (Gramm-Rudman-Hollings Act).

Sets forth procedures for expedited congressional consideration of a proposed cancellation.

Authorizes the President up to 45 days after he transmits a special message to Congress to: (1) withhold discretionary budget authority; and (2) suspend implementation of any targeted tax benefit proposed to be repealed.

Provides for an additional 45-day extension of any discretionary budget authority, item of direct spending, or targeted tax benefit, as applicable.

Requires the chairs of the House Committee on Ways and Means and the Senate Committee on Finance (chairs) to: (1) review any revenue or reconciliation bill or joint resolution amending the Internal Revenue Code being prepared for filing by a conference committee; (2) identify whether such legislation contains any targeted tax benefits; and (3) provide the conference committee with a statement identifying such targeted benefits or declaring that such measure does not contain targeted tax benefits.

Allows legislation reported from the conference committee that includes targeted tax benefits to include the statement of the chairs in a separate section of such legislation in a specified manner.

Authorizes the President, with or without such separate section, to include his statement in such legislation in the same manner if it is signed into law but only with respect to targeted tax benefits in that law.

Requires the Comptroller General to report to Congress on whether any discretionary budget authority is not made available for obligation or item of direct spending or targeted tax benefit continues to be suspended after the President's deferral authority established in this Act has expired.

Terminates this Act on October 1, 2012.

(Sec. 3) Amends the Congressional Budget Act of 1974 to require the Director of the Congressional Budget Office (CBO) to: (1) prepare an estimate of the savings in budget authority or outlays resulting from a proposed cancellation relative to the most recent levels calculated, consistent with the methodology used to calculate a baseline under the Gramm-Rudman-Hollings Act and included in the President's budget submission; and (2) transmit such estimate to the chairs.

(Sec. 4) Expresses the sense of Congress that no President or any executive branch official should condition the inclusion or exclusion, or threaten to condition the inclusion or exclusion, of any proposed cancellation in any special message under this Act upon any vote cast or to be cast by any Member of either Chamber.