Hydroelectric projects offer opportunities for infrastructure development and economic growth; yet, if not well designed, implemented and operated, they have the potential to negatively affect the health and well-being of local and distant downstream communities. Remote rural populations are particularly vulnerable to the sudden influx of men, materials and money, and associated population mixing that accompany project construction phases. Two large-scale baseline health surveys, carried out in 2001/2002 in two communities that were affected by the Nam Theun 2 hydroelectric project in central Lao PDR, were analysed. For the population to be resettled on the Nakai plateau it was observed that access to clean water and basic sanitation facilities was lacking. Faecal examinations revealed a high infection prevalence for Ascaris lumbricoides (67.7%), but relatively low prevalences for hookworm (9.7%), Taenia spp. (4.8%), Enterobius vermicularis (4.4%), Trichuris trichiura (3.9%), Strongyloides stercoralis (1.4%) and Opisthorchis viverrini (0.9%). For the population in the Xe Bang Fai downstream area, rapid diagnostic tests for malaria carried out in the rainy season found a prevalence below 1%, which might be explained by the complete coverage of households with insecticide-treated nets (99.8%). Anthropometric measurements in both populations suggest that wasting, stunting and underweight in under 5-year-old children were moderate to high; 15.9-17.5%, 40.4-55.7% and 35.8-55.7%, respectively. One out of six individuals aged above 14 years were malnourished, most likely as a result of early childhood wasting. Moderate anaemia, assessed by age- and sex-specific haemoglobin levels, was present in 43.8% (Nakai) and 54.9% of the individuals examined (Xe Bang Fai). Several indicators were extracted that can be utilised for monitoring changes in health, well-being and equity, as the project is implemented and operated.