This study was carried out to compare the concentration of heavy metals in blood and DNA damage among children living in an informal e-waste processing village (exposed village) and a reference village in Northern Vietnam. The results revealed that the blood levels of nickel and arsenic in the children at the exposed village were significantly higher than those at the reference village at p < 0.05; however, no significant differences were observed for lead, cadmium, and chromium in children’s blood between the two villages. The overall levels of five heavy metals in exposed children’s blood were significantly higher than those in non-exposed children at p < 0.001. The DNA damage of the children at the exposed village was significantly greater compared to that of the children at the reference village at p < 0.001. The overall blood metal level of the children at both villages was positively correlated with DNA damage given as Tail Length (Spearman r = 0.249, n = 80, p < 0.05), indicating that a higher level of DNA damage could be induced by higher heavy metal exposure among children. It was found that heavy metal pollution from e-waste processing activities could be a potential risk posing to children’s health.