The shift from traditional fee-for-service to value-based payment requires major capital investment. Rural hospitals may be challenged by the volume-to-value transition because they may lack resources necessary to support new delivery models. As a result, many rural hospitals have considered affiliations with larger, better-funded regional health systems. However, rural hospital leaders often struggle to find the appropriate balance between local decision-making control and health system affiliation requirements. In this policy paper, we examine rural hospital and health system motivations for affiliation and present a non-exhaustive list of common affiliation structures with representative examples. Although hospital affiliation can take many forms, rural hospital leaders should develop a thoughtful strategy that weighs the benefits of affiliation versus independence.