This study investigated the relationship between human platelet alloantigen (HPA) polymorphisms of glycoprotein IIb/IIIa and hemorrhagic fever with renal syndrome (HFRS). HPA-1 and HPA-3 genotyping was performed with allele-specific primer polymerase chain reaction in 104 patients with HFRS and 100 normal individuals as controls. The relationships between gene polymorphisms of HPAs and HFRS and the disease severity were analyzed. The results indicated no significant difference in HPA-1 genotype distributions (p > 0.05), but a significant difference in the distributions of genotype and allele frequencies of HPA-3 between HFRS patients and controls (p < 0.01). The distributions of HPA-3 genotype and allele frequencies differed significantly between patients with different clinical types and the HPA-3 b allele was more frequently observed in patients with more severe clinical types. These results indicate that HPA-3 polymorphism may be one of the inherited risk factors associated with the susceptibility of hantavirus infection and the disease severity of HFRS.