To describe the factors associated to stunting in <5-year-old Yanomami Brazilian children, and to evaluate the association of short maternal stature to their offspring's stunting. A cross-sectional study carried out in three villages in the Yanomami territory. We performed a census, in which all households with children < 5-years-old were included. The length/height-for-age z-score <-2 standard deviations was used to classify the children as stunted. Short maternal height was defined as <145 cm for adult women, and <-2 standard deviations of the height-for-age z-score for adolescent women. We used adjusted Poisson regression models to estimate prevalence ratios (PR) along the 90% confidence interval. We evaluated 298 children. 81.2% of children suffered from stunting and 71.9% of the mothers from short stature. In the bivariate analysis, a significant association of stunting with short maternal stature, gestational malaria and child's place of birth were observed. Considering the variables of the children under five years of age, there were significant associations with age group, the child's caregiver, history of malaria, pneumonia, and malnutrition treatment. In the adjusted hierarchical model, stunting was 1.22 times greater in the offspring of women with a short stature (90% CI: 1.07-1.38) compared to their counterparts. Brazilian Amazonian indigenous children living in a remote area displayed an alarming prevalence of stunting, and this was associated with short maternal height, reinforcing the hypothesis of intergenerational chronic malnutrition transmission in this population. In addition, children above 24 months of age, who were born in the village healthcare units and who had had previous treatment in the past for stunting presented higher rates of stunting in this study.