Addressing maternal and child undernutrition is a priority for the National Nutrition Program of Ethiopia. In a cross-sectional design, we selected mother-child pairs (n = 630) from Halaba, south Ethiopia (n = 413, two communities) and Zeway, Oromiya region (n = 217, one community). These communities were previously included in a project to improve agricultural practices. We aimed to estimate the level of maternal and child undernutrition in the two study sites and compare findings to regional/national reports. We also examined associations with gender, household-structure and nutrition/health related variables. Households were selected using simple random sampling based on list of households obtained from local health posts. Mothers were interviewed via questionnaire. Anthropometric measurements were taken from mothers-child pairs. Maternal undernutrition (% BMI<18.5) ranged from moderate (14% Zeway) to high (22% Halaba). In the children, stunting and underweight were very high (54% and 42% stunting, 36% and 21% underweight, in Halaba and Zeway, respectively). Up to 95% of Halaba and 85% of Zeway mothers reported "same as usual" or "less than usual" consumption patterns during their most recent pregnancy compared to periods of non-pregnancy. Mothers reported (61% in Halaba, 18% in Zeway) abstaining from consumption of certain nutritious foods for cultural reasons. Gender and socio-economic-demographic structure of the households, including imbalance of power, control of farm produce, physiological density, household size and dietary habits during pregnancy showed significant associations with maternal and child undernutrition (p<0.05). The levels of child and maternal undernutrition, particularly in children, were unexpected and of concern, given that a national nutrition program has been in place since 2008. The study provides insights for policy makers to improve women's education, reproductive health services for better family planning, and strengthen nutrition/health programs designed to target vulnerable segments of the population in these and other rural communities and districts with similar structure and demographics in Ethiopia.