Study Purpose Hemophagocytic lymphohistiocytosis (HLH) is a life-threatening disease of severe hyperinflammation caused by uncontrolled proliferation of activated lymphocytes and macrophages. In this study, we aimed to explore the genetic factors involved in the pathogenesis of both acquired and familial type HLH. Method The ION TORRENT semi-conductor sequencing method was used to sequence samples from 10 patients who were diagnosed or highly suspected of HLH. Then SNP rs2303116 of STXBP2 genotyping was performed by Sanger sequencing method on samples from 24 patients with HLH and 182 normal controls. Genotype frequencies were then compared and tested by multivariate logistic regression. Finally, the potential impact of rs2303116 on splicing factor binding ability was evaluated using the ESEfinder 3.0 online tool. Results A total of 92 variants were identified in 10 HLH patients, of which 24 variants were rare variants (MAF < 0.01), while the remaining 68 variants were common variants (MAF > 0.01). Among them, 8 different genetic variations in the STXBP2 sequence were identified. We focused on the synonymous SNP rs2303116, as 30% of patients had CT/TT genotype. SNP genotyping was further performed on 24 HLH patients and 182 healthy control cohorts, and the results indicated a significantly elevated CT/TT genotype frequency of rs2303116 in HLH patients compared with healthy controls (patients 37.5% VS. controls 13.2%, P=0.009, OR=3.900, 95% CI 1.537-9.899). Multivariate logistic regression analysis indicated that being female ( OR 0.350, 95% CI 0.143-0.861, P=0.018) and of an older age (> 43y, OR 0.312, 95% CI 0.118-0.822, P=0.014) were independent protective factors, and the rs2303116 CT/TTgenotype (OR 3.900, 95% CI 1.537-9.899, P=0.009) was an independent risk factor for HLH pathogenesis. By comparing the clinical parameters between HLH patients with CT/TT and CCgenotypes, we found that the patients with CT/TT genotype had significantly lower levels of fibrinogen, indicating more aggravated macrophage activation. In silico analysis of splice factor binding to rs2303116 CT/TT genotypes showed significant decrease for SRSF1 but increase for SRSF6, which suggested abnormal splicing machinery was associated with HLH pathogenesis. Conclusion Our study demonstrated for the first time that HLH patients had significantly higher frequencies of the STXBP2 gene polymorphism rs2303116 variant compared with a healthy Chinese Han population, through clinical comparisons and further predictions we suggested regulation of alternative splicing by alleles of SNP rs2303116 could be involved in HLH pathogenesis.