This study was aimed to explore whether the perforin gene 1 (PRF1) mutation is the basis of genetic susceptibility to pathogenesis of acquired severe aplastic anemia (SAA). DNA exon2 and exon3 of PRF1 gene in peripheral blood mononuclear cells in 31 SAA patients and 15 normal controls were amplified by PCR; the sequencing was performed by using ABI pRISM 373OXL sequencer; the mutation loci were sought through checking sequences with GenBank-reported sequences; after the mutation sequences were found, those were cloned into M13 phage vector, then the corresponding sequences of gained 2 chromosomes were sequenced respectively to determine the distribution of different mutations on chromosomes. The results showed that (1) one homozygous mutation (822 C > T, synonymous mutation) and one heterozygous mutation (907 G > A, methionine 303 valine) were found in PRF1 coding region of 2 SAA patients. These mutations were not detected in normal controls. (2) 1 SNP (rs885822) in the coding region was detected in SAA patients and controls, and the heterozygosity rate between the 2 groups was different (p < 0.05). It is concluded that perforin gene mutation may be one risk factor in the aberrant proliferation and activation of cytotoxic T cells in pathogenesis of a part of patients with aplastic anemia.