UNESCO consulted The World Health Organization (WHO) about the possibility of establishing an organization for facilitating more coordination in the planning and timing of international medical congresses. An agreement between WHO and UNESCO was made for the establishment of a permanent Council for Coordination of International Medical Congresses. The Council was formally constituted at a jointly-sponsored conference in Brussels in 1949 as a non-governmental organization, with financial assistance from the two parent organizations, WHO and UNESCO.

The purpose of the Council was described as being to facilitate the exchange of views and scientific information in the medical sciences by securing continuity and coordination between international organizations of medical sciences, by making their work known, and by providing them with material aid where necessary. This was to be achieved through the exchange of information and by the provision of material and financial assistance to congresses and to the individuals attending them.

The scope of activities of the Council was gradually broadened to include other forms of international collaboration in medical sciences in addition to the coordination of congresses. Consequently, in 1952 the name of the Council was changed to the Council for International Organisations of Medical Sciences (CIOMS) and its statutes were revised.