To amend the Internal Revenue Code of 1986 to repeal the new carryover basis rules in order to prevent tax increases and the imposition of compliance burdens on many more estates than would benefit from repeal, to retain the estate tax with a $3,500,000 exemption, to reinstitute and update the Pay-As-You-Go requirement of budget neutrality on new tax and mandatory spending legislation, enforced by the threat of annual, automatic sequestration, and for other purposes.

Division A: Permanent Estate Tax Relief for Families, Farmers, and Small Businesses Act of 2009 - Permanent Estate Tax Relief For Families, Farmers, and Small Businesses Act of 2009 - (Sec. 2) Repeals provisions of the Economic Growth and Tax Relief Reconciliation Act of 2001 (EGTRRA) eliminating the tax on estates and generation-skipping transfers and the step-up in basis provisions for property acquired from a decedent for estates of decedents dying after 2009 (thus retaining estate and gift tax provisions in effect in 2009). Declares that the sunset provision (general termination date of December 10, 2010) of EGTRRA shall not apply to the estate and gift tax provisions of that Act (thus preventing a reversion to estate and gift tax provisions in effect prior to its enactment).

(Sec. 3) Amends the Internal Revenue Code to establish a permanent $3.5 million exclusion amount and a maximum tax rate of 45% for decedents dying, and gifts made, after December 31, 2009.

Division B: Statutory Pay-As-You-Go Act of 2009 - Statutory Pay-As-You-Go Act of 2009 - (Sec. 104) Requires a Pay-As-You-Go (PAYGO) Act to include by reference an estimate of its budgetary effects as determined by the Congressional Budget Act of 1974 (CBA), if timely submitted for printing in the Congressional Record by the chairs of the congressional budget committees (chairs) before the vote on it.

Requires: (1) the Clerk of the House of Representatives or the Secretary of the Senate, as applicable, also to incorporate by reference such printed estimate into the enrollment of a PAYGO Act; and (2) budgetary effects that are not so included to be determined by the Office of Management and Budget (OMB) estimates.

Amends the CBA to require the chairs to request from the Director of the Congressional Budget Office (CBO) an estimate of the budgetary effects of a PAYGO Act before a vote in either chamber on it that, if determined in the affirmative, would clear it for enrollment.

Directs the chairs to post such estimate on their respective committee websites and cause it to be printed in the Congressional Record under "PAYGO ESTIMATE."

Requires CBO to make specified estimate adjustments when calculating budgetary effects of certain designated legislation affecting current policy, as detailed in section 7 of this Act.

Requires OMB to maintain and make publicly available a continuously updated document containing two PAYGO scorecards (the first for a 5-year period and the second for a 10-year period for the beginning of each respective budget year) displaying the budgetary effects of PAYGO legislation, applying certain look-back and averaging requirements. Requires OMB to display as a separate addendum the cost estimates of provisions designated in statute as emergency requirements.

(Sec. 105) Requires OMB to: (1) make an annual public PAYGO report, including a up-to-date document containing the PAYGO scorecards, within 14 business days after Congress adjourns to end a session; and (2) prepare for the President an offsetting sequestration order, which the President shall issue if such report shows a debit on either PAYGO scorecard for the budget year.

(Sec. 106) Prescribes requirements for calculating a sequestration for nonexempt direct spending programs, including Medicare payments and certain nonexempt mandatory programs.

(Sec. 107) Prescribes requirements for CBO adjustments of estimates of budgetary effects of PAYGO legislation for legislation affecting current policy for: (1) payments made under title XVIII (Medicare) of the Social Security Act for physician services; (2) the Estate and Gift Tax under the Internal Revenue Code; and (3) the permanent extension of middle-class tax cuts and the Alternative Minimum Tax (AMT) relief under EGTRRA or the Jobs and Growth Tax Relief and Reconciliation Act of 2003.

(Sec. 108) Applies to this Act certain sequestration order requirements of the Balanced Budget and Emergency Deficit Control Act of 1985 (Gramm-Rudman-Hollings Act), as amended by this Act, including the authority of Members of Congress and certain individuals to request an expedited judicial review of a sequestration order.

(Sec. 109) Makes technical and conforming amendments to the Gramm-Rudman-Hollings Act.

(Sec. 110) Exempts from sequestration: (1) low-income subsidies and catastrophic subsidies under Part D (Voluntary Prescription Drug Benefit Program) of the Social Security Act (SSA); and (2) qualified individual (QI) premiums for Medicare cost-sharing for certain dual eligible low-income Medicare beneficiaries under SSA title XIX (Medicaid).

(Sec. 111) Amends the Gramm-Rudman-Hollings Act to specify additional Social Security, veterans, Tier I Railroad Retirement benefits and other programs and activities exempt from a sequestration order as well as certain economic recovery programs.