Background: In sub-Saharan Africa, urban informal settlements are rapidly expanding, leading to overcrowding and constituting challenging environments for food and water supplies, health and nutrition. The study objectives were to characterise and compare two low-income areas of Nairobi according to socioeconomic (including livestock and gender) indicators and the nutritional status of non-pregnant women of reproductive age and 1 to 3 year-old children; and to investigate socioeconomic predictors of malnutrition in these areas. Methods: In this cross-sectional survey 205 low-income households in deprived areas of Dagoretti and Korogocho (Nairobi) were randomly selected. Socioeconomic data were collected via an interviewer-administered questionnaire. Maternal and child dietary data were collected by a 24-h dietary recall. Maternal and child anthropometric and haemoglobin measurements were taken. Chi-square, t-test and Wilcoxon-Mann-Whitney test were used to compare groups and multivariable linear regression to assess predictors of malnutrition. Results: Dagoretti consistently showed better socioeconomic indicators including: income, education and occupation of household head, land ownership, housing quality and domestic asset ownership. Animal ownership was more than twice as high in Dagoretti as in Korogocho (53.0 % vs 22.9 % of households; p-value < 0.0001). A double burden of malnutrition existed: 41.5 % of children were stunted, and 29.0 % of women were overweight. In addition, 74.0 % of the children and 25.9 % of the women were anaemic, and were at risk of inadequate intakes for a number of micronutrients. Nutritional status and nutrient intakes were consistently better in Dagoretti than Korogocho; height-for-age (0.47 Z-scores higher; p-value = 0.004), the minimum dietary diversity (80.0 % vs 57.7 % in children, p-value = 0.001) and intakes of several nutrients were significantly higher. Positive predictors of maternal nutritional status were income, age and not having a premature delivery. Positive predictors of child nutritional status were area, household head education, mother not being married, female animal ownership and child's sex (female).