Communicable diseases, alone or in combination with malnutrition, account for most deaths in complex emergencies. Factors promoting disease transmission interact synergistically leading to high incidence rates of diarrhoea, respiratory infection, malaria, and measles. This excess morbidity and mortality is avoidable as effective interventions are available. Adequate shelter, water, food, and sanitation linked to effective case management, immunisation, health education, and disease surveillance are crucial. However, delivery mechanisms are often compromised by loss of health staff, damage to infrastructure, insecurity, and poor co-ordination. Although progress has been made in the control of specific communicable diseases in camp settings, complex emergencies affecting large geographical areas or entire countries pose a greater challenge. Available interventions need to be implemented more systematically in complex emergencies with higher levels of coordination between governments, UN agencies, and non-governmental organisations. In addition, further research is needed to adapt and simplify interventions, and to explore novel diagnostics, vaccines, and therapies.