To examine the prevalence of stunting and overweight in children and identify demographic, socio-economic and maternal characteristics, as well as biochemical indicators, associated with these outcomes. A population-based, cross-sectional study was performed. Data from structured questionnaires, anthropometric measurements, and blood and stool samples were used in Poisson regression models to estimate prevalence ratios (PR) according to a hierarchical conceptual framework. Acrelândia, western Brazilian Amazon. Children (n 1139) aged <10 years. Prevalence of stunting was 7·1 % (95 % CI 5·1, 9·6 %) and 3·7 % (95 % CI 2·4, 5·7 %) among children aged <5 years and ≥5 years, respectively; overweight was detected in 20·6 % (95 % CI 17·4, 24·2 %) and 9·4 % (95 % CI 7·2, 12·1 %) of children aged <5 years and ≥5 years, respectively. Among children <5 years of age, stunting was positively associated with the lowest maternal height tertile (PR = 3·09, 95 % CI 1·26, 7·63), low birth weight (PR = 2·70, 95 % CI 1·41, 5·19), diarrhoea for ≥3d (PR = 2·21, 95 % CI 1·03, 4·77) and geohelminth infections (PR = 2·53, 95 % CI 1·02, 6·13). Overweight in children <5 years of age was positively associated with caesarean delivery (PR = 1·45, 95 % CI 1·02, 2·06), birth weight ≥3500 g (PR = 1·82, 95 % CI 1·30, 2·55) and Fe deficiency (PR = 1·64, 95 % CI 1·07, 2·53). Among children aged ≥5 years, land or livestock ownership (PR = 1·85, 95 % CI 1·07, 3·22), maternal overweight (PR = 2·06, 95 % CI 1·23, 3·47), high C-reactive protein concentration (PR = 2·43, 95 % CI 1·26, 4·70), vitamin A deficiency (PR = 1·97, 95 % CI 1·13, 3·41) and high serum TAG concentration (PR = 2·16, 95 % CI 1·27, 3·68) were associated with overweight. Overweight was more prevalent than stunting, being associated with higher household wealth, maternal overweight, caesarean delivery, high birth weight, micronutrient deficiencies and high TAG concentration. Improvements in maternal and child health care with sustainable access to healthy food are necessary to reduce short- and long-term health complications related to overweight in this population.