Incentives for vertical integration in the health care industry have led many hospitals to consolidate into health systems and profess a desire for closer alignment with affiliated physicians. In this study of fourteen organized delivery systems and their 11,000 physicians in sixty-nine medical groups, we found that many health systems did not align well with physicians. Even systems ostensibly committed to alignment emphasized structural relationships that did not enhance physician-system alignment and paid inadequate attention to issues of importance to physicians. This gap between the goal and reality of physician-system alignment appears to be the result of systems' responding to a changing mix of policies, not all of which foster integration.