The IMDI executive board determines the policy and is responsible for the day to day operations of the initiative. Chairman of the board is Cor Spreeuwenberg.

The IMDI Supervisory Council keeps supervision on the societal result of IMDI.NL, the realisation of its goals and according policies and strategy. The supervisory council consists of the medical scientific and technical scientific leaders of the IMDI CoREs and is chaired by independent chairman Anne Flierman.

The IMDI Advisory Council advises the initiative on strategic and practical affairs. The council consists of Anne Flierman, Chris Oomen and Maarten Buijs.