Children are exposed to Hg from mothers (via placenta and lactation), environment (food), and in many parts of the world by thimerosal-containing vaccines (TCV) during immunization. Neurodevelopment studies based on infant hair-Hg (HHg) have been designed without explicit attention to the factors associated with changes in infant physiology and Hg sources of exposure. A longitudinal study of changes in HHg concentrations from birth to 5 years was done in a sample of children from Porto Velho (Rondonia), Brazilian Amazonia. The study extracted information from the asymmetry associated with maternal and infant HHg changes at specified sampling: birth (fetal exposure), 6 months of exclusive breastfeeding, 36 months (weaning) and 60 months (pre-school). The distribution of HHg in breastfed infants followed a pattern different from their mothers. While mothers had the highest HHg concentrations at childbirth, infants showed the highest HHg values at 6 months after the recommended full schedule (six shots) of immunization with TCV; after that, the downward trend in HHg shown by children coincided with both weaning and less frequent vaccination period (5 years). Extended lactation (up to 36 months) was not significantly associated with HHg of infants or mothers; however, significant association (Spearman's r) between maternal and infant HHg concentration was seen at birth (r=0.3534; P=0.001), 6 months (r=0.4793; P<0.0001), 3 years (r=0.0122; P=0.012) and 5 years (r=0.0357; P=0.005). Maternal postpartum metabolic changes, infant development and transitional diets and possibly Hg from TCV contribute to the asymmetry of HHg changes between mothers and children.