Low- to middle-income countries may experience the occurrence of a dual burden of under and overnutrition. To better understand the overall progression of body mass index (BMI) during childhood, we estimated average BMI-for-age z-score (BAZ) growth curves in a population-based longitudinal study of 255 children living in the Brazilian Amazon. Children were aged 0.1–5.5 years at recruitment (2003). We collected data on socio-economic and maternal characteristics, children's birthweight and infant feeding practices. Child anthropometric measurements were taken in 2003, 2007 and 2009. BAZ differences among categories of exposure variables were calculated at 6 and 12 months, and 2, 7 and 10 years. At baseline, the mean (standard deviation) age was 2.6 (1.4) years; 12.9% were overweight and 3.9% thin. After adjustment, mean BAZ estimates were mostly negative. Boys were close to the median value for BAZ until 12 months, whereas girls were below the median (P = 0.05). Children from households above the wealth median were 0.36 z- and 0.49 z-less underweight than poorer children at 7 and 10 years, respectively (P < 0.01). Maternal BMI was positively associated with children's BAZ since 12 months old; BAZ in children from overweight mothers was higher by 0.69 compared with their counterparts at 10 years (P < 0.01). Birthweight was positively related to BAZ up until 2 years (P = 0.01). Socio-economic background and maternal nutritional status are important predictors of BAZ throughout childhood. Although excessive weight gain is a public health concern, it is critical to restrict inequities, while promoting healthier growth in developing countries.