To investigate the correlation between the HLA genes and pathogenesis of aplastic anemia (AA), polymerase chain reaction with specific sequence primers (PCR-SSP) method was used to HLA typing in 82 patients with AA and 400 normal healthy individuals as control. The results showed that A*2301 (1.84%), B*5501 (4.36%) and DRB1*0901 (23.48%) gene frequency in AA patients were significantly higher than those in controls (relative risk: RR=5.0253, 3.3645, 2.1269, chi2=4.6634, 6.3120, 9.1511 respectively) (p<0.01). In contrast, DRB1*1301 (1.23%) gene frequency was significantly lower in AA than that in controls, RR=0.2257, chi2=6.6629 (p<0.01). It is concluded that A*2301, B*5501 and DRB1*0901 genes may be considered as the risk markers while DRB1*1301 gene as a protective marker of AA.