Children's Health Insurance Program Reauthorization Act of 2009 - (Sec. 3) Makes the amendments made by this Act effective on April 1, 2009, regardless of whether final regulations have been promulgated to carry them out.Allows certain state plans under titles XIX (Medicaid) or XXI (State Children's Health Insurance Program) (SCHIP, referred to in this Act as CHIP) of the Social Security Act (SSA) that require state legislation to meet additional requirements imposed by this Act additional time to make required plan changes.Provides for coordination of CHIP funding for FY2009.Title I: Financing - Subtitle A: Funding - (Sec. 101) Amends SSA title XXI to reauthorize the CHIP program through FY2013 at increased levels. (Sec. 102) Provides for the determination of allotments for the 50 states, the District of Columbia, and the commonwealths and territories for FY2009-FY2013.(Sec. 103) Establishes in the Treasury the Child Enrollment Contingency Fund for payments to a state to eliminate its shortfall (the amount by which its available federal CHIP allotments are not adequate to cover its CHIP expenditures).(Sec. 104) Directs the Secretary of Health and Human Services to make a performance bonus payment to states to offset additional Medicaid and CHIP child enrollment costs resulting from enrollment and retention efforts. Limits the use of such payments to reducing the number of low-income children who do not have health insurance coverage in the state. Makes appropriations for FY2009 for such payments. Requires certain funds transfers to cover FY2009-FY2013. (Sec. 105) Reduces the availability of allotments for FY2009 and each ensuing fiscal year from three to two years.(Sec. 106) Amends SSA title XXI to require redistribution of unused allotments to states with funding shortfalls for fiscal years beginning with FY2007.Revises requirements for the redistribution of unused allotments for FY2006.(Sec. 107) Allows qualifying states the option to receive the enhanced portion of the CHIP matching rate for Medicaid coverage of certain children.Repeals the March 31, 2009, termination date of (thus making permanent) the authority for a state to use certain funds to pay for medical assistance to individuals under age 19 whose family income exceeds 150% of the poverty line.(Sec. 108) Makes a one-time appropriation of additional funds to the Secretary of Health and Human Services for FY2013.(Sec. 109) Revises funding requirements for the territories under CHIP and Medicaid for FY2009-FY2013.Removes federal matching payments for data reporting systems from the overall limit on payments to Puerto Rico, the Virgin Islands, Guam, the Northern Mariana Islands, and American Samoa.Directs the Comptroller General to report to the appropriate congressional committees on federal funding under Medicaid and CHIP for such territories.Subtitle B: Focus on Low-Income Children and Pregnant Women - (Sec. 111) Gives states the option to cover targeted low-income pregnant women under CHIP through a state plan amendment if certain conditions are met, including that the state has established an income eligibility level of at least 185% of the federal poverty line for pregnant women under Medicaid. Sets the minimum income eligibility level for children under age 19 at 200% of the poverty line applicable to a family of the size involved. Provides for automatic enrollment for children born to women receiving pregnancy-related assistance.(Sec. 112) Provides for phase-out of CHIP coverage for nonpregnant childless adults, leaving states an option to apply for a Medicaid waiver to continue coverage for such adults. Requires extension of an expiring waiver at state request, but only through calendar 2009 and only for childless adults who were covered through that year. Prescribes terms and conditions for coverage of parents of targeted low-income children.Directs the Comptroller General to study and report to Congress on whether: (1) the coverage of a parent, a caretaker relative, or a legal guardian of a targeted low-income child under a state CHIP health plan increases the enrollment of, or the quality of care for, children; and (2) such parents, relatives, and legal guardians who enroll in such a plan are more likely to enroll their children in such a plan or in a state Medicaid plan.(Sec. 113) Eliminates counting Medicaid child presumptive eligibility costs against CHIP allotment.(Sec. 114) Limits the matching rate for states that propose to cover children with effective family income that exceeds 300% of the poverty line. Exempts from this denial (grandfathers) any state that already has an approved state plan amendment or waiver to provide such expenditures. (Sec. 115) Allows the Secretary, at state option, to provide the state with the federal medical assistance percentage determined for the state for Medicaid with respect to certain expenditures or otherwise made to provide medical assistance under Medicaid to a child who could be covered by the state under CHIP.Allows a state to cover: (1) certain individuals and thereby receive federal financial participation for medical assistance for them under Medicaid; or (2) receive such federal financial participation for children made eligible as a result of an income or resource eligibility level expansion.Title II: Outreach and Enrollment - Subtitle A: Outreach and Enrollment Activities - (Sec. 201) Amends SSA title XXI to direct the Secretary to award grants during FY2009-FY2013 for outreach and enrollment efforts to increase the enrollment and participation of eligible children under CHIP and Medicaid.Makes appropriations for FY2009-FY2013. Directs the Secretary to develop and implement a national enrollment campaign to improve the enrollment of underserved child populations in CHIP and Medicaid programs.Allows payments under CHIP and Medicaid for translation or interpreting services in connection with the enrollment of, retention of, and use of services by, individuals for whom English is not their primary language.(Sec. 202) Amends SSA title XI to provide for increased outreach and enrollment of Indians in CHIP and Medicaid.Waives the 10% cap on CHIP payments for outreach with respect to any expenditures for outreach activities to families of Indian children likely to be eligible for child health assistance under the state Medicaid plan or related waivers.(Sec. 203) Authorizes a state plan under the Medicaid and CHIP programs to rely on findings from an Express Lane agency to conduct simplified eligibility determinations.Amends SSA title XIX to authorize a federal or state agency or private entity in possession of the sources of data directly relevant for Medicaid eligibility determination (including eligibility files maintained by an Express Lane agency) to convey such information to the state Medicaid agency, if such conveyance meets specified requirements. Prescribes civil and criminal penalties for improper disclosure of such information.Directs the Secretary to enter into agreements necessary to permit a state that elects the Express Lane option to receive data directly relevant to determining eligibility and the correct amount of benefits under CHIP or Medicaid from: (1) the National Directory of New Hires; and (2) data regarding enrollment in insurance that may help to facilitate outreach and enrollment under the state Medicaid and CHIP plans and such other programs as the Secretary may specify.Subtitle B: Reducing Barriers to Enrollment - (Sec. 211) Gives states the option, as an alternative to the current documentation requirement, to verify a declaration of U.S. citizenship or nationality for purposes of Medicaid or CHIP eligibility through verification of a name and Social Security number with the Commissioner of Social Security. Prescribes a procedure for investigating any inconsistency between the name and number presented and the name and number in the records maintained by the Commissioner.Applies such documentation requirements to CHIP.Makes appropriations to the Commissioner of Social Security to carry out such responsibilities.(Sec. 212) Requires state child health insurance plans to describe procedures used to reduce administrative barriers to enrollment of children and eligible pregnant women under Medicaid or CHIP.(Sec. 213) Requires the Secretary, in order to assure continuity of coverage, to develop a model process for the coordination of the enrollment, retention, and coverage under Medicaid and CHIP of children who frequently change their state of residency or otherwise are temporarily located outside of their state of residency.(Sec. 214) Permits states to waive certain restrictions which result in a five-year delay for coverage of necessary health services for children and women residing lawfully in the United States under the Medicaid program and CHIP.Title III: Reducing Barriers to Providing Premium Assistance - Subtitle A: Additional State Option for Providing Premium Assistance - (Sec. 301) Gives states the option to provide a premium assistance subsidy for qualified employer-sponsored coverage to all targeted low-income children eligible for CHIP who have access to such coverage, if the child (or the child's parent) voluntarily elects to receive such a subsidy. Allows employers to opt-out of being paid the subsidy directly, in which event the state shall pay the employee.Amends SSA title XIX to allow a state to elect to offer a similar voluntary premium assistance subsidy for qualified employer-sponsored coverage to all individuals under age 19 entitled to Medicaid.Directs the Comptroller General to study and report to Congress on cost and coverage issues relating to any state premium assistance programs for which federal Medicaid and CHIP matching payments are made.(Sec. 302) Requires state CHIP plans to describe procedures in place to provide outreach, education, and enrollment assistance for families of children likely to be eligible for premium assistance subsidies under CHIP.Waives the 10% cap on CHIP payments for outreach activities to families of children likely to be eligible for premium assistance payments under the state child health plan or related waivers.Subtitle B: Coordinating Premium Assistance With Private Coverage - (Sec. 311) Amends the Internal Revenue Code to require a group health plan to permit an employee who is eligible, but not enrolled, for coverage under the plan to enroll if either of the following conditions are met: (1) the employee or dependent covered under Medicaid or CHIP has coverage terminated as a result of loss of eligibility, and the employee requests coverage under the group health plan within 60 days after such termination; or (2) the employee or dependent becomes eligible for Medicaid or CHIP assistance if the employee requests coverage within 60 days after the eligibility determination date.Directs the Secretary and the Secretary of Labor jointly to establish a Medicaid, CHIP, and Employer-Sponsored Coverage Coordination Working Group to: (1) develop the model coverage disclosure form; and (2) identify impediments to the effective coordination of coverage available to families.Title IV: Strengthening Quality of Care And Health Outcomes of Children - (Sec. 401) Amends SSA title XI to direct the Secretary to identify and publish for general comment an initial, recommended core set of child health quality measures for use by state Medicaid and CHIP programs, health insurance issuers and managed care entities that contract with such programs, and item and service providers. Directs the Secretary to identify existing quality of care measures for children that are: (1) in use under public and privately sponsored health care arrangements; or (2) part of reporting systems that measure both the presence and duration of health insurance coverage over time.Directs the Secretary to establish a pediatric quality measures program to improve and strengthen such initial core child health care quality measures.Directs the Secretary to award: (1) grants and contracts for the development, testing, and validation of new, emerging, and innovative evidence-based measures for children's health care services; and (2) up to 10 grants to states and child health providers for demonstration projects to evaluate promising ideas for improving the quality of children's health care and the use of health information technology. Specifies funding.Directs the Secretary to conduct a childhood obesity demonstration project. Authorizes appropriations for FY2008-FY2012.Directs the Secretary to establish a program to encourage the development and dissemination of a model electronic health record format for children enrolled in a state Medicaid or CHIP plan.Requires the Institute of Medicine to study and report to Congress on pediatric health and health care quality measures.Makes FY2009-FY2013 appropriations to carry out this section. Increases the matching rate for collecting and reporting on child health measures.(Sec. 402) Specifies the information each state must cover in its annual CHIP report to the Secretary, including eligibility criteria, enrollment, and retention data.Requires the Comptroller General to study and report to the appropriate congressional committees on children's access to primary and specialty services under Medicaid and CHIP.(Sec. 403) Requires a state child health plan to provide for application of certain managed care quality safeguards to CHIP coverage, state agencies, enrollment brokers, managed care entities, and managed care organizations in the same manner such safeguards are applied under the Medicaid program.Title V: Improving Access to Benefits - (Sec. 501) Requires the child health assistance provided to a targeted low-income child to include coverage of dental services necessary to prevent disease and promote oral health, restore oral structures to health and function, and treat emergency conditions.Gives states with a separate CHIP program the option to provide dental-only supplemental coverage for any child enrolled in a group health plan or employer-offered health insurance coverage who would otherwise satisfy the requirements for a targeted low-income child under a state child health plan. Allows a state child health plan, at state option, to waive a waiting period for a child provided dental-only supplemental coverage. Requires the Secretary to develop, through entities that fund or provide prenatal care services to targeted low-income children under CHIP, a program to deliver oral health educational materials that inform new parents about risks for, and prevention of, early childhood caries and the need for a dental visit within their newborn's first year of life.Directs the Secretary to work with states, pediatric dentists, and other dental providers to include on the Insure Kids Now website (http://www.insurekidsnow.gov/) and hotline (1-877-KIDS-NOW) a current and accurate list, updated quarterly, of all such dentists and providers within each state that provide dental services to children enrolled in the state plan (or waiver) under Medicaid or CHIP, together (on the website) with a description of the services.Directs the Comptroller General to study and report to Congress on children's access to dental services in underserved areas and to oral health care. (Sec. 502) Provides for the parity of mental health services in CHIP plans with all covered medical and surgical benefits.(Sec. 503) Applies the prospective payment system (PPS) to services provided by federally-qualified health centers (FQHCs) and rural health clinics.(Sec. 504) Requires a state child health plan to afford individuals enrolled under it a grace period of at least 30 days from beginning of a new coverage period to make premium payments before the individual's coverage under the plan may be terminated.(Sec. 505) Provides that nothing in SSA title XXI shall be construed as limiting a state's ability to provide child health assistance for covered items and services that are furnished through school-based health centers.(Sec. 506) Establishes the Medicaid and CHIP Payment and Access Commission (MACPAC) to: (1) review policies of Medicaid and CHIP affecting children's access to covered items and services; and (2) report and make recommendations to Congress concerning them. Authorizes appropriations. Title VI: Program Integrity and Other Miscellaneous Provisions - Subtitle A: Program Integrity and Data Collection - (Sec. 601) Applies a minimum FMAP of 90% to expenditures related to administration of payment error rate measurement (PERM) requirements applicable to CHIP.Waives the 10% cap on CHIP administrative costs for all expenditures related to the administration of PERM requirements.Prohibits the Secretary from calculating or publishing any national or state-specific error rate based on the application of PERM requirements to CHIP until after a final rule implementing such requirements is in effect for all states. Specifies requirements for any calculation of a national error rate or a state specific error rate after such a final rule is in effect for all states.Requires the final rule implementing the PERM requirements to include: (1) clearly defined criteria for errors for both states and providers; (2) a clearly defined process for appealing error determinations by review contractors or specified agency and personnel; and (3) clearly defined responsibilities and deadlines for states in implementing any corrective action plans.Directs the Secretary to review the Medicaid Eligibility Quality Control (MEQC) requirements with PERM requirements and coordinate consistent implementation of both sets of requirements, while reducing redundancies.Prescribes requirements for a state option to substitute data resulting from the application of the PERM requirements to the state for data obtained from the application of MEQC requirements to the state, and vice versa, for specified purposes.Directs the Secretary to establish state-specific sample sizes for application of the PERM requirements with respect to state child health plans beginning with FY2009.(Sec. 602) Appropriates increased amounts for FY2009 for data collection regarding low-income children without health insurance coverage.Requires the Secretary of Commerce, among other things, to make appropriate adjustments to the Current Population Survey (CPA) to: (1) develop more accurate state-specific estimates of the number of children enrolled under Medicaid; and (2) include health insurance survey information in the American Community Survey (ACS) related to children.Authorizes the Secretary to transition to the use of all, or some combination of, ACS estimates, instead of the CPS, if the Secretary of Commerce so recommends.(Sec. 603) Directs the Secretary, directly or through contracts or interagency agreements, to conduct an independent subsequent evaluation of 10 states with approved child health plans. Makes FY2009 appropriations for such evaluation.(Sec. 604) Revises requirements for audits of state CHIP programs. Declares that the Comptroller General (as well as the Secretary and the Office of Inspector General), for evaluation and audit purposes, shall have access to any books, accounts, and other documents related to the expenditure of federal CHIP funds that are in state or local government, grantee, or contractor possession, custody, or control.(Sec. 605) Declares that: (1) nothing in this Act allows federal payment for individuals who are not lawfully residing in the United States; and (2) SSA titles XI, XIX (Medicaid), and XXI (CHIP) provide for the disallowance of federal financial participation for erroneous expenditures under Medicaid and under CHIP, respectively.Subtitle B: Miscellaneous Health Provisions - (Sec. 611) Amends the Deficit Reduction Act of 2005 to make a technical amendment to the requirement to provide early and periodic screening, diagnostic, and treatment (EPSDT) services for all children in benchmark benefit packages.(Sec. 612) Amends the Medicare, Medicaid, and SCHIP Balanced Budget Refinement Act of 1999 to repeal the requirement that the Secretary refer to CHIP as SCHIP or the state children's health insurance program. (Sec. 613) Prohibits the Secretary from approving any new health opportunity account demonstration programs.(Sec. 614) Provides that, only for purposes of computing the FMAP for a state for a fiscal year, beginning with FY2006, and applying it under Medicaid, any significantly disproportionate employer pension or insurance fund contribution shall be disregarded in computing the state's per capita income, but shall not be disregarded in computing the per capita income for the continental United States (and Alaska) and Hawaii.Prohibits any state from having its FMAP reduced as a result of the application of this section.Directs the Secretary to report to Congress on: (1) the problems presented by the current treatment of pension and insurance fund contributions in the use of Bureau of Economic Affairs calculations for the FMAP and for Medicaid; and (2) possible alternative methodologies to mitigate such problems.(Sec. 615) Provides that nothing in the prohibition on use of voluntary contributions, and the limitation on use of provider-specific taxes to obtain federal financial participation under Medicaid, shall be construed by the Secretary as prohibiting a state's use of funds as the nonfederal share of Medicaid expenditures where such funds are transferred from or certified by a publicly-owned regional medical center located in another state, so long as the Secretary determines that such use is proper and in the interest of the Medicaid program.(Sec. 616) Amends SSA title XIX, as amended by the Medicare Improvements for Patients and Providers Act of 2008, to extend the Medicaid disproportionate share hospital (DSH) allotments for Hawaii and Tennessee. (Sec. 617) Directs the Comptroller General to report to Congress on the extent to which state payment rates for Medicaid managed care organizations under Medicaid are actuarially sound.Subtitle C: Other Provisions - (Sec. 621) Establishes a task force to conduct a nationwide campaign of education and outreach for small business concerns regarding the availability of coverage for children through private insurance options, the Medicaid program, and CHIP.(Sec. 622) Expresses the sense of the Senate that it: (1) recognizes the necessity to improve affordability and access to health insurance for all Americans; (2) acknowledges the value of building upon the existing private health insurance market; and (3) affirms its intent to enact legislation this year that, with appropriate consumer protections, improves access to affordable and meaningful health insurance coverage for employees of small business and individuals.Title VII: Revenue Provisions - (Sec. 701) Amends the Internal Revenue Code to increase excise tax rates on cigars, cigarettes, cigarette papers and tubes, smokeless tobacco, pipe tobacco, and roll-your-own tobacco. Imposes a tax on floor stocks of tobacco products (other than certain cigars and cigarette papers and tubes), reduced by a $500 tax credit. Requires payment of such floor stock taxes on or before August 1, 2009. Extends the floor stock tax to articles located in a foreign trade zone on any tax increase date.(Sec. 702) Applies administrative tax law provisions relating to permits, inventories, reporting, and recordkeeping to manufacturers and importers of processed tobacco (i.e., any tobacco other than tobacco products).Expands the authority of the Secretary of the Treasury to deny, suspend, or revoke permits for manufacturing or importing tobacco products.Revises the definition of "roll-your-own tobacco" to include cigars or cigar wrappers.Amends the Tariff Act of 1930 to apply limitation periods for assessment of tax under the Internal Revenue Code to alcohol and tobacco excise taxes. Imposes an immediate excise tax on any tobacco products, cigarette paper, or tubes produced in the United States at any place other than the premises of a lawful manufacturer of such products. (Sec. 703) Directs the Secretary of the Treasury to study and report to Congress on: (1) the magnitude of tobacco smuggling in the United States; and (2) any recommendations for the most effective steps to reduce it.(Sec. 704) Amends the Tax Increase Prevention and Reconciliation Act of 2005 to increase by 0.5% the amount of any required installment of corporate estimated tax otherwise due in July, August, or September 2013.