Issues surrounding mother-to-child transmission of HIV/AIDS pose considerable challenges in complex humanitarian emergencies. The risk of vertical transmission through breastfeeding is well recognised, but safe alternatives are limited by the social, economic and environmental conditions of emergency situations. In 2000, the World Health Organisation published a technical report on behalf of the UNFPA/UNICEF/WHO/UNAIDS Inter-agency Task Team on Mother-to-child Transmission of HIV which outlined revised recommendations for infant feeding by HIV-positive women. This paper outlines reasons why these recommendations may be insufficient during the initial stages of complex humanitarian emergencies and proposes recommendations for establishing infant-feeding policy. Methods of mother-to-child transmission of HIV are reviewed and recent research findings are discussed. Rationale for modifying the 2000 UNFPA/UNICEF/WHO/UNAIDS infant-feeding recommendations in complex emergency situations is explored from the perspective of the infant, the mother and humanitarian field staff. Ethical limitations and future priorities are considered. The paper concludes with recommendations and a policy decision-making framework for consideration during the initial stages of humanitarian crises.