Deficit Reduction and Effective Legislative Line Item Veto Act of 2006

Deficit Reduction and Effective Legislative Line Item Veto Act of 2006 - Amends the Congressional Budget and Impoundment Control Act of 1974 (CBICA) to authorize the President to propose the cancellation (line item veto) of any dollar amount of discretionary budget authority or targeted tax benefit within 10 days after its enactment.

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

Provides for adjustment of: (1) committee allocations resulting from such rescission; and (2) 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 rescission.

Authorizes the President temporarily to: (1) withhold discretionary budget authority (including emergency spending); and (2) suspend implementation of any targeted tax benefit proposed to be repealed.

Amends the Gramm-Rudman-Hollings Act to extend: (1) pay-as-you-go requirements through FY2011; and (2) certain expiring provisions through FY2016.

Amends Rule XXIII (Code of Official Conduct) of the House to prohibit a Member from conditioning the inclusion in any legislation of language to fund a district-oriented earmark, a particular project, or a limited tax benefit on any vote cast by the Member in whose district the project will be carried out.

Requires the Joint Committee on Taxation to review any revenue measure, reconciliation bill, or joint resolution for limited tax benefits, and identify them and their beneficiaries, including their sponsors.

Amends Rule XIII (Calendars and Committee Reports) to make it generally out of order for the House to consider a bill or joint resolution until 24 hours, or for legislation containing a district-oriented earmark or limited tax benefit until three business days, after copies of such measure (and any accompanying report) are available.

Amends Rule XXII (House and Senate Relations) to apply the same requirements to a conference report.

Amends Rule XXII to: (1) make a motion to request or agree to a conference on a general appropriation bill in order only if the Senate expresses its disagreements with the House in the form of numbered amendments; (2) require all provisions on which the two Chambers disagree to be open to discussion at any meeting of a conference committee; and (3) make it out of order to consider conference reports not reflecting resolutions of differences between the two Chambers, as approved.