A birth cohort study was conducted in Khan Hoa Province, central Vietnam between 2009 and 2012 to determine the seroprevalence of hepatitis B virus (HBV) in pregnant women and their children, and associated risk factors. We enrolled 1987 pregnant women with their babies at the birth phase, and 12.6% (95% confidence interval [CI]: 11.1-14.0) of mothers were hepatitis B surface antigen (HBsAg)+. At 2-year follow-up phase, 1339 (67.4%) children were enrolled of whom 76.6% completed hepatitis B vaccines (HepB) and 1.9% (95% CI: 1.2-2.7) were HBsAg+. When mothers were hepatitis B e antigen (HBeAg)+, 28.3% of children have got infected even with complete HepB. HBV infection in mothers, hepatitis B surface antibody (anti-HBs antibody) below the seroprotective level in children, and mothers with pre-pregnancy low body mass index were associated with HBV infection in children. Meanwhile, HBV infection in children, older maternal age, no or incomplete doses of HepB, and boys were associated with anti-HBs antibody below the seroprotective level in children. Our birth cohort study determined a low rate of congenital HBV infection and associated risk factors in Vietnam, however further studies are needed to advance prevention including anti-viral therapy in pregnant women at high risk.