Previous studies of chordoma have focused on either surgery, radiotherapy, or particular tumor locations.This paper reviewed the outcomes of surgery and proton radiotherapy with various tumor locations.Between 2001 and 2008,40 patients with chordomas of the skull base and cervical spine had surgery at our hospital.Most patients received proton therapy.Their clinical course was reviewed.Age, sex, tumor location, timing of surgery, extent of resection,and chondroid appearance were evaluated in regard to the progression-free survival (PFS) and overall survival (OS).The primary surgery (PS) group was analyzed independently.The extensive resection rate was 42.5%.Permanent neurological morbidity was seen in 3.8%.Radiotherapy was performed in 75% and the mean dose was 68.9 cobalt gray equivalents.The median followup was 56.5 months.The 5-year PFS and OS rates were 70% and 83.4%,respectively.Metastasis was seen in 12.5%.The tumor location at the cranio-cervical junction (CCJ) was associated with a lower PFS (P=0.007).In the PS group, a younger age and the CCJ location were related to a lower PFS (P=0.008 and P<0.001, respectively).The CCJ location was also related to a lower OS (P=0.043) and it was more common in young patients (P=0.002).Among the survivors, the median of the last Karnofsky Performance Scale score was 80 with 25.7% of patients experiencing an increase and 11.4% experiencing a decrease.Multimodal surgery and proton therapy thus improved the chordoma treatment.The CCJ location and a younger age are risks for disease progression.