Medical Homes Act of 2009 - Directs the Secretary of Health and Human Services to establish a three-year demonstration project under titles XIX (Medicaid) and XXI (Children's Health Insurance Program) (CHIP, formerly known as SCHIP) of the Social Security Act for the implementation of a patient-centered medical home program to improve the effectiveness and efficiency in providing Medicaid and CHIP assistance to an estimated 500,000 to 1 million targeted beneficiaries.