Objectives: The theory of ecological unequal exchange explains how trade and various forms of economic activity create the problem of environmental degradation, and lead to the deterioration of population health. Based on this theory, our study examined the inter-relationship among economic characteristics, ecological footprints, CO2 emissions, infant mortality rates and under-5 mortality rates in low-income countries. Design: A longitudinal ecological study design. Setting: Sixty-six low-income countries from 1980 to 2010 were included in the analyses. Data for each country represented an average of 23 years (N=1497). Data sources: Data were from the World Development Indicators, UN Commodity Trade Statistics Database, Global Footprint Network and Polity IV Project. Analyses: Linear mixed models with a spatial power covariance structure and a correlation that decreased over time were constructed to accommodate the repeated measures. Statistical analyses were conducted separately by sub-Saharan Africa, Latin America and other regions. Results: After controlling for country-level sociodemographic characteristics, debt and manufacturing, economic activities were positively associated with infant mortality rates and under-5 mortality rates in sub-Saharan Africa. By contrast, export intensity and foreign investment were beneficial for reducing infant and under-5 mortality rates in Latin America and other regions. Although the ecological footprints and CO2 emissions did not mediate the relationship between economic characteristics and health outcomes, export intensity increased CO2 emissions, but reduced the ecological footprints in sub-Saharan Africa. By contrast, in Asia, the Middle East and North Africa, although export intensity was positively associated with the ecological footprints and also CO2 emissions, the percentage of exports to high-income countries was negatively associated with the ecological footprints. Conclusions: This study suggested that environmental protection and economic development are important for reducing infant and under-5 mortality rates in low-income countries.