Carbon ion radiation therapy (RT) is available at the German Ion Research Center (GSI) in Darmstadt, Germany, since December 1997. Patient treatments within the pilot project are carried out by radiation oncologists of the University of Heidelberg in cooperation with the Department of Biophysics of GSI, the Division of Medical Physics of the German Cancer Research Center Heidelberg and the Research Center Rossendorf. Patients are treated within three beam time blocks of 20 days per year at the basic physics research center at GSI, the overall capacity per year being 45 to 50 patients. Main purpose of the pilot project was to investigate carbon ion radiation therapy for different tumor entities within clinical phase I/II trials. This manuscript updates the results of the clinical phase I/II trial of carbon ion RT in chordomas and low grade chondrosarcomas of the skull base and summarizes the current status of the ongoing phase I/II trial for extracranial chordomas and low grade chondrosarcomas.