Background This study aimed to ascertain the Social Determinants (SDs) of malnutrition (over and undernutrition) of Chilean children aged up to five. Methods The study was carried out using a sample of children from zero to five years old (n = 1,270,485; 52.2% female) from the National Socioeconomic Characterization Survey (CASEN) 2017. A multinomial logistic regression model was used, where the "child nutritional status" outcome variable assumed three possible values: normal nutrition, overnutrition, and undernutrition, while taking those variables reported in previous literature as independent variables. Results The model, by default, set normal nutrition as the reference group, Count R2 = 0.81. Results show a higher likelihood of both overnutrition and undernutrition among male children from the lowest quintiles, with native ethnic backgrounds, reporting health problems, having public health insurance, and who attend kindergarten. Additionally, higher probabilities of undernutrition in younger than two and living in the north of the country, while overnutrition is more likely in the south. Conclusions Socioeconomic variables are fundamentally related to both over and undernutrition; the current single schema program to prevent malnutrition should consider SDs such as ethnicity and geographical location, among others; moreover, successful nutritional programs-which focused on the lowest quintiles, need to be expanded to other vulnerable groups and pay more attention to overnutrition.