Objective:To investigate the clinical significance of homeobox gene D3 ( HOXD3) expression in glioma and its biological functions. Methods:A total of 1001 patients with glioma collected from Chinese Glioma Genome Atlas (CGGA) and the Cancer Genome Atlas (TCGA) were chosen in our study; their clinical data and transcriptome data were retrospectively analyzed. One-way analysis of variance was used to evaluate the differences of HOXD3 expressions in different pathological grading of glioma. These patients were divided into HOXD3 low expression group and HOXD3 high expression group according to the average value of HOXD3 expression. Kaplan-Meier survival analysis was used to compare the differences in survival time between patients from the HOXD3 high-expression group and HOXD3 low-expression group. Univariate and multivariate Cox regression analyses were used to investigate the effect of HOXD3 on the prognoses of patients with glioma. Gene ontology (GO) analysis, Kyoto encyclopedia of genes and genomes (KEGG) and gene set enrichment analysis (GSEA) were used to investigate the biological function of HOXD3. Pearson correlation analysis was used to analyze the correlation between HOXD3 expression and expressions of other genes. Results:(1) The expression level of HOXD3 gradually increased with the increase of pathological grading of glioma (in the CGGA data, the expression levels in grading II, III and IV gliomas were 0.737±0.085, 1.323±0.125 and 1.652±0.083, respectively; in TCGA data, the expression levels in grading II, III and IV gliomas were 0.082±0.008, 0.177±0.014 and 0.259±0.016, respectively). The HOXD3 expression levels among different pathological grading of glioma were statistical different ( P<0.05). (2) As compared with that in the HOXD3 low-expression group, the survival time of patients in the HOXD3 high-expression group was significantly shorter ( P<0.05). CGGA data showed that the HOXD3 expression ( HR=1.348, 95%CI: 1.171-1.552, P=0.000), tumor grading ( HR=2.793, 95%CI: 1.981-3.936, P=0.000) and isocitrate dehydrogenase 1 ( IDH1) mutation status ( HR=0.689, 95%CI: 0.492-0.964, P=0.029) were independent influencing factors for prognoses of glioma patients. TCGA data showed that the HOXD3 expression ( HR=2.147, 95%CI: 1.252-3.681, P=0.005), age ( HR=1.036, 95%CI: 1.026-1.046, P=0.000), tumor grading ( HR=3.178, 95%CI: 2.299-4.392, P=0.000) and IDH1 mutation status ( HR=0.440, 95%CI: 0.317-0.613, P=0.000) were independent influencing factors for prognoses of glioma patients. (3) GO, KEGG and GSEA analyses showed that HOXD3 was closely related to the cell cycle; the HOXD3 expression was positively correlated with various cell cycle associated genes ( P<0.05). Conclusion:HOXD3 is an independent influencing factor for prognoses of glioma patients, whose biological function is related to the periodic regulation of glioma.