The aim of this study was to identify nutritional factors and households characteristics associated with child stunting, maternal overweight and the familial coexistence of both types of malnutrition. In Guatemala, 2000, with nationally representative data, we selected 2261 households with at least one child aged 12-60 months and his/her mother. Nutritional status was assessed in children (e.g., stunting as height-for-age Z-score < -2) and mothers (e.g., overweight as body mass index >= 25 kg/m2) and identified the presence of both, child stunting and maternal overweight in the same household (SCOM). With logistic regression models we assessed the association of the malnutrition indicators with individual and household socio-economic and health characteristics. SCOM was identified in 18% of households. Socio-economic status (SES) of SCOM households was significantly lower than SES of households with non-stunted children. SCOM households, compared to those with normal-stature children and normal weight mothers, were more likely to have mothers of short stature (adjusted odds ratio-OR ± 95% CI = 3.1 (2.1-4.7)), higher parity (1.2 (1.1-1.3)), currently working (1.7 (1.1-2.6), and self-identified as indigenous (2.0 (1.3-3.1)). Factors associated with stunting in children such as poverty, maternal short stature and indigenousness, were predictors of SCOM. These findings support the notion that SCOM is an extension of the malnutrition spectrum in the most disadvantaged population groups in countries that are in the middle of their nutrition transitions such as Guatemala. At the same time it revealed that these populations are already in the stage of chronic, nutrition related diseases associated with less physical activity and more access to highly processed foods of low cost, high dietary energy and low nutrient density in important population groups. The challenge for the decision makers and service deliverers is to guide SCOM households to deal equally with both extremes of the malnutrition continuum.