Isocitrate dehydrogenase (IDH) gene mutation is one of the most exciting new advances in these years. It has been reported that IDH gene frequently altered in grade II and grade III gliomas. We aimed to identify the mutation frequency of IDH genes in Chinese anaplastic glioma patients, the association of IDH gene mutation with other clinical and molecular pathological features and the prognostic value of it. We performed polymerase chain reaction-based IDH gene mutation detection in 203 anaplastic glioma patients from China. A total of 108 and 3 patients harbored IDH1 and IDH2 gene mutation, respectively. And there was a higher proportion of MGMT promoter methylation, frontal lobe location, and better outcome and lower proportion of temporal location in IDH-mutated samples. There were hardly any significant association between protein expression level of well-known markers and IDH mutation. Anaplastic oligoastrocytoma and anaplastic astrocytoma patients with IDH gene mutation showed similar prognosis with anaplastic oligodendroglioma patients with wild-type IDH gene. IDH gene mutation is a good prognostic marker and a potential substratification factor for anaplastic glioma patients.