Abstract This paper seeks to reveal the institutional interests of the Council of Ministers, the European Parliament and the Commission in the comitology system. This is done by an investigation of the 2006 comitology reform, which introduced the regulatory procedure with scrutiny. This reform was the result of developments in four areas: the Lamfalussy reform in the area of financial regulation; the controversial use of comitology in the area of GMOs, food safety and the environment; the failed Constitutional Treaty; and the amending of the 1999 comitology decision. The analysis shows that the reform was the result of a two-dimensional constitutional struggle. The first dimension concerns the relative supervisory position of the two legislative actors, the Council and the European Parliament. The second dimension concerns the relationship between the legislative and the executive branch of the EU system. In theoretical terms, the analysis demonstrates an example of T.M. Moe's 'politics of structural choice'. The paper ends by drawing lessons for the negotiations on the new comitology system following the Lisbon Treaty.