To know the prevalence and probable causes of breakthrough hepatitis B virus (HBV) infection among children born after the introduction of universal infant hepatitis B vaccination in Shandong province, China. The subjects of this study were selected from the provincial hepatitis B serosurvey conducted in 2006, who were born between 1992 and 2005 (aged 1-15 years) and were confirmed to have completed three or more doses of hepatitis B vaccine. Finally 3527 subjects were involved in this study and were investigated using a unified question are. Blood samples were collected from them to detect hepatitis B surface antigen (HBsAg), antibody against HBsAg (Anti-HBs) and antibody against hepatitis B core antigen (Anti-HBc). The parents of children positive for HBsAg were followed up. Blood samples were collected from their parents to detect for HBsAg. The rate and correlative factors of breakthrough HBV infection were gotten by single-factor and multiple-factor analysis. For the 3527 subjects, the overall prevalence rates of breakthrough HBV infection were 3.15% (111/3527), which decreased while birth year grew (χ(2)(Trend) = 44.83, P < 0.01) , the rate of subjects born in 1992 was the highest (9.9%, 16/161) , subjects born in 2000 was the least (0.8%, 2/258) , the rate of the self-report positive HBsAg status of mother, father and the other family members (15.22%, 7/46;34.09%, 15/44;17.65%, 6/34) were higher than the negative (2.99%, 104/3481, 2.76%, 96/3483, 3.01%, 105/3493) (χ(2) values were 22.28, 13.97, 23.68, respectively, all P values were < 0.01) , timely first dose of hepatitis B vaccine (5.37%, 41/763) was higher than the subjects that not in time (2.53%, 70/2764) (χ(2) = 15.596, P < 0.01) . The overall prevalence rates of breakthrough chronic HBV infection was 1.08% (38/3527), which decreased while birth year grew (χ(2)(Trend) = 9.96, P < 0.05) , the rate of subjects born in 1992 was the most (3.1%, 5/161) , subjects born in 1997 was the least (0.4%, 1/261) , the rate of the self-report positive HBsAg status of mother, father and the other family members (13.04%, 6/46;29.55%, 13/44;17.65%, 6/34) were higher than the negative (0.92%, 32/3481;0.72%, 25/3483;0.92%, 32/3493) (χ(2) values were 62.62, 338.80, 88.44, respectively, all P values were < 0.05) , timely first dose of hepatitis B vaccine (1.83%, 14/763) was lower than the subjects that not in time (0.87%, 24/2764) (χ(2) = 5.16, P = 0.02) . Multiple factors analysis showed that compared to the negative, the self-report positive HBsAg status of father, mother increased the risk of breakthrough HBV infection,OR (95%CI) values were 3.73 (1.09-12.75) and 26.76 (11.86-60.37) , respectively (all P values were < 0.05) , compared with eastern cities, the risk of western cities were the highest (OR (95%CI) = 6.00 (2.50-14.40) , P < 0.05) the risk of children born in 1992-2001 was higher than those born in 2002 ( (OR (95%CI) = 1.91 (1.10-3.32) , P < 0.05) . Compared to the negative, the self-report positive HBsAg status of father, mother and the other family members increased the risk of breakthrough chronic HBV infection,OR (95%CI) values were 7.51 (1.44-39.17) , 99.99 (34.29-291.62) , 8.94 (1.81-44.10) , respectively (all P values were < 0.05) , compared with eastern cities, the risk of western rural areas were the highest (OR (95%CI) = 12.51 (2.78-56.25) , P < 0.05) , sharing tooth brush with the others increased the risk (OR (95%CI) = 8.67 (1.14-66.14) , P < 0.05) . Among HBsAg-positive children, those with HBsAg positive mother and father accounted for 12/23 and 6/19, respectively. The prevalence of breakthrough HBV infection and breakthrough chronic HBV infection among children was low in Shandong province. Mother to infant transmission might be the main reason for the infection while the role of the horizontal transmission within the family shouldn't be ignored.