Epstein-Barr virus associated hemophagocytic lymphohistiocytosis (EBV-HLH) has a high mortality rate among children. The pathogenesis of, and underlying predisposing factors for, EBV-HLH are as yet unclear; however, natural killer cells may play a key role in progression of the disease. This study attempted to determine whether killer cell immunoglobulin-like receptor (KIR) gene polymorphisms are responsible for susceptibility to EBV-HLH. Of the 125 children with EBV infection studied, 59 had EBV-HLH and 66 patients had EBV associated infectious mononucleosis (IM) without HLH. The control group was 146 normal children without immune deficiency. KIR polymorphisms were determined by polymerase chain reaction with sequence-specific primers. KIR polymorphism data were analyzed using the X2 test or Fisher's exact test. The overall observed carrier frequency (OF) of KIR2DS5 was significantly higher in EBV-HLH patients than in IM patients and normal controls (49.2% versus 31.8%, P = 0.048; 49.2% versus 31.5%, P = 0.018, respectively), and the odds ratios (95% confidence interval) were 2.071 (1.0014.286) and 2.101(1.1323.900) respectively. The OF of KIR3DS1 was significantly higher in the EBV-HLH patients than in the IM patients (47.4% versus 24.6%, P = 0.012), but not different from normal controls. In summary, KIR polymorphisms may be involved in the development of EBV-HLH, with KIR2DS5 promoting susceptibility to this disease. The obtained KIR data will enrich the understanding of genetic relationships among diseases associated with EBV infection in children.