Medicaid Accountability through Transparency Act of 2009 - Amends title XIX (Medicaid) of the Social Security Act, as amended by the Children's Health Insurance Program Reauthorization Act of 2009, to direct the Secretary of Health and Human Services to implement a program under which the Secretary shall make available through the public Internet website of the Department of Health and Human Services non-aggregated, de-identified information on individuals collected under the Medicaid Statistical Information System (MSIS).
Requires reduction of Medicaid payments to states which have not provided for electronic transmission of claims data in the format specified by the Secretary and consistent with the MSIS (including detailed individual enrollee encounter data and other information that the Secretary may find necessary).
Directs the Secretary to report to specified congressional committees on the feasibility, potential costs, and potential benefits of making publicly available through an Internet-based program de-identified payment and patient encounter information for items and services furnished under title XXI (Children's Health Insurance Program) (CHIP, formerly known as SCHIP) of the Social Security Act which would not otherwise be included in the information collected under the MSIS.