Discussion of the flaws of the current fee-for-service health care reimbursement model has become commonplace. Health care costs cannot be reduced without moving away from a system that rewards providers for providing more services regardless of need, effectiveness, or quality. What alternatives are likely under health care reform, and how will they impact the challenged finances of academic medical centers? Bundled payment methodologies, in which all providers rendering services to a patient during an episode of care split a global fee, are gaining popularity. Also under discussion are concepts like the advanced medical home, which would establish primary care practices as a regular source of care for patients, and the accountable care organization, under which providers supply all the health care services needed by a patient population for a defined time period in exchange for a share of the savings resulting from enhanced coordination of care and better patient outcomes or a per-member-per-month payment. The move away from fee-for-service reimbursement will create financial challenges for academic medicine because of the threat to clinical revenue. Yet academic health centers, because they are in many cases integrated health care organizations, may be aptly positioned to benefit from models that emphasize coordinated care. The author also has included a series of recommendations for how academic medicine can prepare for the implementation of new payment models to help ease the transition away from fee-for-service reimbursement.