Background: The simultaneous presence of undernutrition and over-nutrition represents a paradox in global public health and is of increasing concern in Ecuador, where chronic malnutrition and overweight and obesity occur in the context of demographic and epidemiologic transitions. Two overlapping trends are present in Ecuador; while levels of stunting have decreased slowly in the past three decades, increasing proportions of children <5 years and women of reproductive age suffer from overweight and obesity. Aim: To analyze stunting and overweight and obesity in children <5 and their mothers aged from 15 to 49 years in the context of demographic and household characteristics between 1986 and 2012. Methods: This study compares data from nationally-representative surveys conducted in Ecuador in 1986, 2004, and 2012, each of which collected information on children <5 and mothers aged 15-49 years. Results: The prevalence of chronic malnutrition in children <5 decreased at different rates among Ecuadorians who differ in terms of residence, socioeconomic status, and mothers’ level of education, while overweight and obesity increased dramatically in the same period. Conclusion: Chronic malnutrition in children <5 and overweight in children <5 and mothers 15-49 years represent a double burden of malnutrition in Ecuador. The phenomena differ in their effects, and, while the prevalence of stunting is declining in Ecuador as it is in many parts of the world, the problem of overweight and obesity has emerged in dramatic fashion, and currently represents an extraordinary challenge to public health.