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,P<0.05) and between groupⅠ and the control group (χ2=9.513,P<0.05). No evident differences of TNF-α -238 A were found between group Ⅱ and control group (χ2=0.047,P>0.05); the significant differences of IFN-γ +874 A allele frequency were found between groupⅠ and groupⅡ(χ2=7.238,P<0.05), and between groupⅠ and the control group (χ2=5.199,P<0.05). No evident differences were found between groupⅡ and the control group (χ2=0.602,P>0.05); the significant differences of IL-4 -590 C/T allele frequency were not found between groupⅠand group Ⅱ(χ2=0.632,P>0.05), also groupⅠ and the control group (χ2=0.584,P>0.05), 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<0.001), and between groupⅡ and the controls (χ2=35.418,P<0.001), but the significant differences were not found between groupⅠand the control group (χ2=1.759,P>0.05). Conclusions This study suggested the possibility that the TNF-α -238 A allele and IFN-γ +874 A allele were associated with HBV intrauterine infection. There was no evident relationship between IL-4 -590 C/T allele SNP and susceptibility to HBV intrauterine infection, but the IL-10 -1082 G allele was associated with preventive efficacy to HBV intrauterine infection.