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The continuing outbreaks of highly pathogenic avian influenza (HPAI) in Southeast Asia have been disastrous to the poultry industry in the region and have raised serious global public health concerns. Risk for animal and human health exists along the whole poultry value chain. The Food and Agricultural Organisation of the United Nations initiated a series of value chain studies in Asia and Africa during 2007 as a means to develop a better understanding of the trade flows, disease transmission mechanisms and possible entry points for intervention in various value chains. This paper outlines the methodology used to undertake these value chain studies, their use in developing policy and HPAI control measures that decrease animal and human health risks, and describes a value chain study in North Sumatra undertaken by FAO and the University of North Sumatra.