Prevention, Awareness, and Research of Autoimmune Disease Act of 2006 - Amends the Public Health Service Act to require the Secretary of Health and Human Services, acting through the Director of the Centers for Disease Control and Prevention (CDC), to award grants to eligible entities to conduct public and professional awareness activities regarding autoimmune diseases, such as lupus, multiple sclerosis, rheumatoid arthritis, and fibromyalgia. Defines an "eligible entity" as a nonprofit organization, a consumer group, an institution of higher education, a federal, state, or local government agency, or a media organization. Allows such an entity to use grant funds to: (1) promote increased awareness of early intervention and treatment to significantly improve the quality of life for people with autoimmune diseases; (2) target minority communities that may be underserved or disproportionately affected by such diseases; and (3) target women to help reduce the amount of time taken for correct diagnosis of such diseases.
Requires the Secretary, acting through the Administrator of the Health Resources and Services Administration (HRSA), to: (1) award grants to eligible entities for the education of health care providers on potential links between autoimmune diseases and cognitive and mood disorders, such as depression; and (2) establish an educational loan repayment program for physicians agreeing to conduct research on autoimmune diseases.