The vision of the malaria control and elimination programme is an Eastern Mediterranean Region in which all countries are malaria-free, except very limited foci in complex and/or border areas in sub-saharan Africa countries, where malaria incidence is very low and not a barrier to social and economic development.

The programme's mission is to support countries in implementing national programmes for the control, elimination and prevention of reintroduction of malaria through universal coverage of at-risk populations through quality assured diagnosis, the provision of effective antimalarial medicines and prevention of reintroduction through effective and rational vector control methods. A strong and comprehensive malaria surveillance, monitoring and evaluation system is crucial for measuring achievement towards this goal.