BACKGROUND: The discovery of isocitrate dehydrogenase 1 and 2 gene (IDH1/2) mutations has enabled grade III glioma to be divided into mutated and wild-type IDH1/2 groups, which are known to carry different prognosis and molecular features. However, detailed subgroup analysis of grade III glioma is limited. To address this, we investigated molecular and prognostic features of grade III glioma with and without IDH1/2 mutation. METHODS: We retrospectively analyzed 115 grade III glioma patients. Clinical parameters were obtained from medical records. The mutation of IDH1/2 and TP53 was analyzed by direct sequencing. O(6)-methylguanine methyltransferase gene (MGMT) gene promoter methylation status was determined by methylation-specific polymerase chain reaction. Detection of chromosome copy number changes of 1p, 7p (EGFR), 9p (CDKN2A), 10q (PTEN), and 19q was carried out by multiple ligation-dependent probe amplification. Patients were divided into two groups, mutated IDH1/2 and wild-type IDH1/2, for correlation with the factors analyzed. RESULTS: In our series, as previously reported, IDH1/2 mutation was an independent prognostic marker for improved progression-free and overall survival (OS) (P < 0.0001 and P < 0.0001, respectively) in patients with grade III gliomas. Subgroup analysis found that incomplete resection, 7p gain, and TP53 mutation were independent prognostic factors of poor outcome in grade III glioma patients with mutated IDH1/2 (P = 0.0092, P = 0.015 and P = 0.026, respectively), while there were none in patients with wild-type IDH1/2. CONCLUSIONS: IDH1/2 gene status was significantly associated with prognosis in grade III gliomas. Subgroup analysis found that poor prognostic factors existed even in patients with IDH1/2 mutation.