The SIB is organised as a federation of bioinformatics research groups from leading Swiss universities and the Swiss Federal Institutes of Technology.

It comprises six major governing bodies:

Foundation Council: is the highest organ of the Institute; represents the interests of SIB institutional partners.
Board of Directors: defines the Institute’s scientific strategy, internal procedures and core bioinformatics resources to be maintained by the Institute
Executive Director: is responsible for the overall management of the Institute
Council of Group Leaders: discusses all matters relating to the Institute’s groups as a whole
Scientific Advisory Board: makes recommendations on the Institute's activities
Financial auditor