The levels of mercury (Hg) and selenium (Se) and their correlation in human scalp hair of 29 pairs of pregnant women and their newborns living at a high-Hg and low-Se area, the Second Song-Hua-Jiang River System, have been studied by instrumental neutron activation analysis. Our results indicate that the Hg level in infant hair samples are roughly close to that in their mothers, whereas the Se level in infants is much higher. Furthermore, the molar ratios of Se/Hg in newborns are also 40% higher than those in mothers. It demonstrates that infants are able to absorb more selenium from their mothers’ bodies to protect against or alleviate the intoxication of Hg. This “autoprotective mechanism” likely plays a critical role during fetal development. The possible chemical species of Hg and Se in hair is also discussed.