Medical Information Protection and Research Enhancement Act of 1999 - Title I: Individual's Rights - Subtitle A: Review of Protected Health Information by Subjects of the Information - Requires specified health entities in possession of protected health information to arrange (except in certain circumstances) for its inspection or copying upon the request of the individual subject of such information (subject individual). Prescribes procedures for: (1) notification upon request denial, including the reasons for such denial, and the concomitant review procedures; (2) requests by such individual to amend such information; and (3) conspicuous disclosure of such entities' confidentiality practices.

(Sec. 103) Directs the Secretary of Health and Human Services (the Secretary) to develop model notices of confidentiality.

Subtitle B: Establishment of Safeguards - Mandates: (1) administrative, technical, and physical safeguards for protected health information; (2) a record of any protected health information disclosures; and (3) identification of disclosed information as protected health information.

Title II: Restrictions on Use and Disclosure - Prescribes guidelines for disclosure of protected health information with respect to: (1) authorizations for treatment, payment, and health care operations; (3) the individual's next of kin and directory information; (4) emergency circumstances; (5) certain oversight agencies; (6) public health authorities; (7) health researchers; (8) civil, judicial, and administrative procedures; (9) certain law enforcement procedures; (10) payment for health care through card or electronic means; (11) certain duly authorized representatives acting on behalf of a subject individual (including a deceased subject individual and a minor); and (12) certain business sales, transfers, or mergers.

(Sec. 213) Precludes permissible disclosures from liability.

Title III: Sanctions - Subtitle A: Criminal Provisions - Amends the Federal criminal code to impose criminal penalties for knowingly and intentionally obtaining or disclosing protected health information in violation of title II of this Act.

Subtitle B: Civil Sanctions - Establishes civil monetary penalties for substantial and material failure to comply with this Act.

(Sec. 312) Prescribes a procedure for imposition and judicial review of such penalties.

(Sec. 313) Grants exclusive enforcement authority to the insurance commissioner of the life insurer's domicile State.

Title IV: Miscellaneous - Preempts, subject to exceptions, any State law relating to matters covered by this Act.

(Sec. 401) Authorizes the Secretaries of Defense and of Transportation to establish exceptions to the disclosure requirements of this Act with respect to Department of Defense and Coast Guard personnel, respectively, pursuant to the Secretaries' determination that exceptions are necessary for national defense purposes.

(Sec. 403) Directs the National Research Council, in conjunction with the Institute of Medicine of the National Academy of Sciences, to study and report to Congress on research issues relating to protected health information.