To date, relatively little work on priority setting has been carried out at a macro-level across major portfolios within integrated health care organizations. This paper describes a macro marginal analysis (MMA) process for setting priorities and allocating resources in health authorities, based on work carried out in a major urban health region in Alberta, Canada. MMA centers around an expert working group of managers and clinicians who are charged with identifying areas for resource re-allocation on an ongoing basis. Trade-offs between services are based on locally defined criteria and are informed by multiple inputs such as evidence from the literature and local expert opinion. The approach is put forth as a significant improvement on historical resource allocation patterns.