Objective: Cytokine storms are central to the development of Epstein-Barr virus-associated hemophagocytic lymphohistiocytosis (EBV-HLH). Previous studies showed that single nucleotide polymorphisms (SNPs) of cytokine genes may be associated with the development of EBV-HLH in children. We investigated the associations between SNPs and haplotypes of interleukin-2 receptor subunit alpha (IL2RA), interleukin-10 (IL-10), interferon gamma (IFN-γ), IFN regulatory factor 5 (IRF5), and C-C chemokine receptor 2 (CCR2) and susceptibility to EBV-HLH in children. Methods: 66 children with EBV-HLH and 58 healthy EBV-seropositive controls were enrolled in the study. SNPs of IL2RA rs2104286, rs12722489, and rs11594656, IL-10 rs1800896, rs1800871, and rs1800872, IFN-γ rs2430561, IRF5 rs2004640, and CCR2 rs1799864 were assayed and genotyped using the SNaPshot technique. Results: The frequencies of the AA genotype and A allele of IL2RA rs2104286 and IL-10 rs1800896, and the CC genotype and C allele of IL-10 rs1800872 were significantly higher in the EBV-HLH group compared with those in the control group, respectively. The frequencies of genotypes and alleles of IL2RA rs2104286, IL-10 rs1800871, IFN-γ rs2430561, IRF5 rs2004640, and CCR2 rs1799864 were similar in both groups. In addition, the IL2RA AGT (rs2104286-rs12722489-rs11594656) and IL-10 ACC (rs1800896-rs1800871-rs1800872) haplotypes were also significantly more frequent in the EBV-HLH group. Conclusions: The SNPs of IL2RA rs2104286, IL-10 rs1800896 and rs1800872 and the haplotypes of IL2RA AGT and IL-10 ACC are highly associated with susceptibility to EBV-HLH in children.