There is an urgent need for measurements of the magnitude and determinants of under-5 mortality at the district level in Indonesia. This article describes a sample household survey conducted in Ende District, East Nusa Tenggara province. Complete birth histories were recorded from all women residing in a sample of 32 villages (7454 households) of Ende. The survey was conducted in early 2010, deriving measures for the period 2000-2009. The survey instrument also included key variables required to measure determinants of under-5 mortality. The results showed that there are significant differentials in under-5 mortality risk within Ende, ranging from 27 to 85 per 1000. This information will assist the district health office to implement maternal and child health programs to meet national targets for United Nations Millennium Development Goal 4. The findings provide robust mortality measures at the district level and demonstrate the feasibility of conducting such a study using local resources, in a short time, and with low costs.