The increased complexity in the public administration has shed light on cross sectoral governance and its challenges. The aim of this study is to investigate how governments organize cross sectoral policy areas. Through a comparison between the Integration Agency and the Gender Equality Agency in Sweden, I investigate how the government has organized the integration policy and the gender equality policy, as well as how the government has argued for the agencies existence. The results show how the policy areas were organized, and the conclusions of the study are that cross sectoral agencies have a difficult mission to work for a policy’s breakthrough in the society, through collaborations with non-defined agencies, municipalities, and organizations. Other agencies tend to not prioritize the cross sectoral policies. Another conclusion is that cross sectoral agencies risk termination when there is a change of government, especially if the creation of the agency lacks a wide support from the parliament. A last conclusion is that the government might react to “problems” in the policy field by both creating a new agency and terminating an existing one. This sheds light on government’s tendency to reform policy as a way of rationalizing and legitimize the policy area.