Perinatal transmission and infection of hepatitis B virus (HBV) in early childhood were observed in the offsprings of hepatitis B surface antigen (HBsAg)-positive mothers who had been vaccinated against HBV immediately after giving birth. This prophylaxis failure of perinatal HBV infection is likely due to the interplay of the virus and host immune response. To investigate whether the HLA polymorphism affected the outcome of the perinatal prophylaxis, HLA class I (HLA-A, Band Cw) and class II (HLA-DRB1, DQA1, DQB1 and DPB1) were typed using serology, PCR-SSOP (polymerase chain reaction-sequence specific oligonucleotide probe), and PCR-ARMS (amplification refractory modification system) methods in 22 HBeAg-positive mothers and their 10 prophylaxis-succeeded and 12 prophylaxis-failed children. The HLA types of the mothers and their children were compared with 198 HBsAg-negative healthy controls in a Korean population. HLA-B35 (relative risk=4.2, p<0.01), B51 (relative risk=3.2, p<0.02), DRB1*07 (relative risk=3.8, p<0.03), and DQA1*02 (relative risk=3.8, p<0.03) alleles were more frequent in HBeAg-positive mothers than in the controls. Also, HLA-DRB1*13 (relative risk=0.1, p<0.02) and DPB1*0401 (relative risk=0.1, p<0.02) alleles were less frequent in HBeAg-positive mothers. However, HLA alleles did not affect the outcome of the perinatal prophylaxis against HBV. These results suggest that the reported influences of some HLA alleles on the natural chronic HBV infections may not operate in the HBV infections in children received perinatal prophylaxis.