Comprehensive Tuberculosis Elimination Act of 2008 - Title I: Department of Health and Human Services in Coordination with the Centers for Disease Control and Prevention and Other Appropriate Agencies - Subtitle A: National Strategy for Combating and Eliminating Tuberculosis - (Sec. 101) Amends the Public Health Service Act to revise the grant program through which the Secretary of Health and Human Services is authorized to carry out programs with respect to the prevention, treatment, control, and elimination of tuberculosis.

Includes research on latent tuberculosis infection within such program.

Includes within such program research and development and related activities to develop new tools for the elimination of tuberculosis and new methods to enhance detection and response to tuberculosis outbreaks. Encourages the Secretary to give priority to programmatically relevant research so that new tools can be utilized in public health practice.

 Includes among demonstration projects the Secretary may carry out as part of such program projects for the development of regional capabilities to prevent, control, and eliminate tuberculosis and prevent multidrug resistant and extensively drug resistant strains of tuberculosis and projects for the intensification of efforts to: (1) reduce health disparities in the incidence of tuberculosis; (2) control tuberculosis along the U.S.-Mexico border; (3) prevent, detect, and treat tuberculosis among foreign-born persons who are in the United States; and (4) prevent, detect, and treat tuberculosis in high-risk populations and settings.

Allows the Secretary, as part of such program, to develop, enhance, and expand information technologies that support tuberculosis control, including surveillance and database management systems with cross-jurisdictional capabilities.

Requires the Secretary, in awarding grants for such tuberculosis programs, to give highest priority to applicants that will contribute nonfederal funds to carry out such activities.

Subtitle B: Interagency Collaboration - (Sec. 111) Expands the duties for the Advisory Council for the Elimination of Tuberculosis to include providing to the Secretary and other appropriate federal officials advice on: (1) coordinating the activities of the Department of Health and Human Services (HHS) and other federal agencies; (2) responding rapidly and effectively to emerging issues in tuberculosis; and (3) efficiently utilizing the federal resources involved. Requires the Council to make or update recommendations on the comprehensive plan to eliminate tuberculosis in the United States. Sets forth reporting requirements for the Council.

Requires the Federal Tuberculosis Task Force to: (1) provide to the Secretary and other appropriate federal officials advice on research into new tools; and (2) make recommendations on the development of a comprehensive plan for the creation of new tools for the elimination of tuberculosis.

Subtitle C: Evaluation of Public Health Authorities - (Sec. 121) Requires the Secretary to: (1) report to the appropriate congressional committees on changes needed to federal and state public health authorities to address current disease containment challenges; and (2) promulgate regulations to update current interstate and foreign quarantine regulations.

Subtitle D: Authorization of Appropriations - (Sec. 131) Authorizes appropriations for FY2009-FY2013. Requires the Secretary to allocate a portion of grant funds on the basis of a formula that takes into account the level of tuberculosis morbidity and case complexity in the respective geographic area.

Title II: National Institutes of Health - (Sec. 201) Allows the Director of the National Institutes of Health (NIH) to expand, intensify, and coordinate research and development and related NIH activities with respect to tuberculosis. Authorizes such activities to include: (1) enhancing basic and clinical research on tuberculosis, including drug resistant tuberculosis; (2) expanding research on the relationship between tuberculosis and the human immunodeficiency virus; and (3) developing new tools for the elimination of tuberculosis, including public health interventions and methods to enhance detection and response to outbreaks of tuberculosis.
Output: To amend the Public Health Service Act with respect to making progress toward the goal of eliminating tuberculosis, and for other purposes.