The aim of this study was to identify the relationship between susceptibility of children to acquired aplastic anemia (AA) and HLA-A, -B, -DRB1 alleles. 80 children with AA were enrolled in this study. Among of them, 34 patients collected from tissue typing test centers of Nanfang Hospital; 46 patients were diagnosed at Department of Pediatrics of Sun Yat-Sen Memorial Hospital. In these patients, 48 were males, 32 were females, and with average age 8.1 years old, 6 cases were non-severe AA (nSAA), 74 case were severe AA (SAA). The healthy control group consisted of 109 donors who were from the same area. All the patients and healthy controls were of Han Chinese, and all were unrelated individuals. The polymerase chain reaction sequence specific primers (PCR-SSP) was used to analyze the polymorphism of HLA-A, -B and -DRB1 alleles. Pearson Chi-square or continuity correction or two-sided Fisher's exact test were used. The results showed that the genotype frequency of HLA-B*48:01 and DRB1*09:01 were significantly higher in children with AA as compared with healthy controls (P < 0.05). The genotype frequency of HLA-B*51:01, DRB1*03:01 and DRB1*11:01 were significantly lower in children with AA as compared with healthy controls (P < 0.05). Besides, the results also demonstrated that the genotype frequencies of HLA-B*48:01 and DRB1*09:01 were significantly higher in SAA as compared with controls, the genotype frequencies of B*51:01, DRB1*03:01 and DRB1*11:01 were significantly lower in SAA, as compared with controls. In conclusion, HLA-B*48:01 and DRB1*09:01 are related with children AA, and may be susceptible alleles to the development of children AA. Besides, the expression of HLA-B*51:01, DRB1*03:01 and DRB1*11:01 are low in children with AA, whether they are relative protection alleles of children needs to be further studied.