OBJECTIVE: Skull base chordomas are clinically malignant because of the difficulty of total removal and the high recurrence rate. Because the disease-free survival after surgery is currently unpredictable, there is a need for new parameters, obtained from histologic analyses of the resection specimen, that allows a risk stratification of patients with chordoma. METHODS: In recent years, electron microscopic diagnoses were introduced into the clinical practice for the diagnosis of chordoma in our department. Clinical outcomes and electron microscopic features were retrospectively reviewed in the study. The electron micrograph shows that clival chordoma can be divided into cell-dense type (CDT) and matrix-rich type (MRT). Of all the patients with chordoma, complete data from 27 patients were obtained. There were 12 patients in the CDT group and 15 patients in the MRT group. The paraffin-embedded tissue samples were stained with Ki-67 antibody. The prognostic values of electron microscopic classification were compared between the 2 groups. RESULTS: There were no statistical differences in the gender (P = 0.704) and age distribution (P = 0.243) between the 2 groups. There was also no statistical difference concerning the constitution of primitive tumors and recurrent tumors between the 2 groups (P = 0.706). The CDT group had a higher mortality rate than the MRT group (P = 0.037). The tumors in the CDT group were prone to recurrence and the need for reoperation within 1 year after surgery, which is statistically different from that in the MRT group (P < 0.001). Chordoma tumors of 23 patients (85.2%) stained positive for Ki-67. CDT chordomas had a higher Ki-67 proliferation index than the MRT chordomas (P = 0.013). CONCLUSIONS: The present study demonstrates the utility of the ultrastructural features in the prognostic outcome of patients with chordoma. According to the ultrastructures of chordomas, they can be divided into CDT and MRT. CDT chordoma cells have a more aggressive proliferative ability. Patients with CDT have a poor prognostic factor in clival chordoma, which has a higher risk of recurrence and a shorter survival.