This article presents an analysis of the mergers in the Danish Higher Education (HE)-sector with a particular emphasis on the 2007 mergers involving universities and Government Research Institutes (GRIs). Furthermore, it follows the post-merger processes up to 2014/2015 at two Danish universities and examines the consequences of the changes seen from the perspective of the key stakeholders, the university managements and the employees. It is shown that the two cases differ in important respects, but also that the three groups of actors within each case have different views of both the processes and the outcomes. Finally, it is shown that it makes a significant difference whether a federal or a unitary structure is implemented after the merger, although each solution has both strengths and weaknesses.