This paper compares state-of-the-art implementation of Cost Benefit Analysis (CBA) and Cost Utility Analysis (CUA) as tools for making priorities in allocation of national public funds in the transport sector and health sector, respectively, in Sweden. These methods have several similarities although they diverge on how to treat effects on health and life length. However, it is shown here that there are considerable differences in how the methods are implemented in the decision process. The paper discusses differences in which cost and benefit components that are included, economic parameters, and the role of economic evaluation in the decision making. We believe that both transport and health sector planners have a lot to learn from each other.