The incidence of HFE gene mutations in myelodysplastic syndrome (MDS) cases remains controversial. In this study, we examined the HFE C282Y and H63D mutations in 271 Chinese patients with MDS, 402 with aplastic anemia (AA) and 1,615 healthy controls by polymerase chain reaction-restriction fragment length polymorphism in combination with DNA sequencing. No C282Y mutations were observed in the entire cohort. The distribution of H63D heterozygous and homozygous genotypes was not significantly different between the AA cases and the controls (9.7% versus 10.2%, 0.25% versus 0.24%, respectively). While the H63D heterozygous genotype in MDS patients was significantly lower than that in the controls (4.1% versus 10.2%, p = 0.002), the H63D homozygous genotype was not detected in the MDS patients. The results suggest that HFE gene mutations are not common genetic factors in Chinese patients with MDS and AA. We also compared iron metabolic parameters, including serum ferritin, serum iron, and transferrin saturation values, between HFE mutant and HFE wild-type groups in the absence of transfusion iron overload, but no significant difference was found in either MDS or AA patients except that the level of serum iron in AA patients was significantly higher in mutant carriers than in those with wild-type HFE (p = 0.011). Similarly, there was no significant difference between HFE mutant and HFE wild-type MDS and AA patients in clinical indices such as alanine aminotransferase, aspartate aminotransferase, fasting blood sugar values, and electrocardiogram. The results suggest that H63D mutations may not have clinical significance in Chinese patients with MDS and AA.