Background The influences of genomic background are confirmed in more diseases. Immunologic tolerance after intrauterine infection of hepatitis B virus is considered to occur in T cells. Cytokines work effectively in eliminating virus by immune system after hepatitis B virus infection. To explore the relationship between cytokines (tumor necrosis factor-α, interferon-γ, interleukin-4 and interleukin-10), which expressed abnormal quantity in the peripheral blood to intrauterine hepatitis B virus infectious children, gene single nucleotide polymorphism (SNP) and susceptibility to hepatitis B virus intrauterine infection. Methods This is a cross sectional study of molecular clinical epidemiology. The subjects in this study were selected from outpatients of hepatitis B vaccine follow-up special clinics of our hospital in the period. According to intrant criteria, the high risk children of hepatitis B virus (HBV) intrauterine infection were divided into immune failure group (group Ⅰ); and immune effective group (group Ⅱ) and non high risk children belonged to the control group. Four gene SNP sites of TNF-α -238, IFN-γ +874, IL-4 -590 and IL-10 -1082 were determined by real-time quantitative fluorescent polymerase chain reaction (PCR). Results The significant differences of TNF-α -238 A allele frequency were found between group Ⅰ and groupⅡ (χ2=6.797,P0.05), and the groupⅡ and the control group (χ2=0.004,P>0.05)respectively; The significant differences of IL-10 -1082 G allele frequency were found between groupⅡ and groupⅠ (χ2=10.359,P