Pillar 3 of the global technical strategy for malaria 2016–2030 calls for the transformation of malaria surveillance into a core intervention in all malaria-endemic countries, as well as in countries which have eliminated malaria but remain susceptible to re-establishment of transmission. This reference manual covers subjects that are relevant to both settings. The target readership of this manual includes staff working in ministries of health, national malaria programmes and health information systems; partners involved in malaria surveillance; and WHO technical officers who advise countries on malaria surveillance.