A cross-sectional study was undertaken to assess the nutritional status of children aged 3–15 y in remote villages of Lao PDR. Study sites were chosen from two provinces: Luang namtha (north) and Sekong province (south). All the sampled 1075 children were measured for anthropometry, following the standard methods. Dietary intake, morbidity and socio-economic data were obtained by interviews with parents. This study confirmed the high prevalence of growth retardation among children, as well as persistent food insecurity in the remote areas of Lao PDR. Prevalence of stunting was 74.1% in Luang namtha and 62.6% in Sekong province, with school-aged children being worse-off than under-five ones. Children's diets were inadequate in quality as well as in quantity, with very limited availability of rice and other food items throughout the year. Our findings also suggest the negative outcomes of government's development programme were often overlooked, and that more attention should be paid on the fragile living conditions in the resettlement villages, especially for the ethnic minority.