Objective: The clinical value and prospective function of hypoxia inducible factor 1 alpha (HIF-1α) in myelodysplastic syndromes (MDS) remain poorly understood. Therefore, the objective of the current investigation was to elucidate the expression level and clinical significance of HIF-1α in MDS. Methods: A total of 94 bone marrow tissues were gathered, including 74 from MDS patients and 20 from healthy donors. Morphological examination, fluorescence in situ hybridization (FISH) and karyotype analysis were carried out to categorize MDS into different subgroups. The expression level of HIF-1α mRNA was detected by fluorescence quantitative real-time RT-PCR. Results: HIF-1α mRNA expression in MDS bone marrow samples was clearly upregulated than that in healthy donors (P<0.001). The HIF-1α mRNA levels increased gradually (P=0.040) in different groups based on the IPSS score from low, intermediate-1, intermediate-2 to a high-risk group. HIF-1α expression in the high-risk group, as evaluated by the percentage of BM blasts, was markedly higher than that in the low-risk group (P=0.021). HIF-1α mRNA expression in the FISH-abnormal group was prominently up-regulated compared to the FISH-normal group (P=0.005). HIF-1α expression in the karyotype-abnormal group was apparently increased compared to that in the karyotypenormal group (P=0.026). Furthermore, Spearman analysis disclosed that HIF-1α expression was positively related to patient prognosis, as assessed by karyotype (r=0.330, p=0.022). Conclusion: HIF-1α may participate in the development of MDS and can lead to poor prognosis.