The goal of this clinical research study is to learn if proton beam therapy, with or without photon beam radiation therapy, is effective in the treatment of skull base chordoma. The safety of this treatment will also be studied.

Proton therapy is a kind of external beam radiation therapy where protons are directed to a tumor site. Researchers are trying to determine what level of proton therapy gives the most benefit without causing toxic side effects. Researchers will also be testing the treatment's effect.

If your doctor feels it is necessary, the proton beam therapy may be combined with standard photon therapy.

If you are eligible to take part in this study, you will receive proton beam therapy at The University of Texas (UT) MD Anderson Cancer Center (MDACC), and possibly photon beam, no sooner than 2 weeks after the last surgery to remove the tumor. You will receive proton beam therapy once a day for about 35 treatments (7 weeks). Treatment will be given for 5 days in a row each week (except for Saturdays, Sundays and holidays) at the MDACC Proton Center in Houston. The whole process should take up to 1 hour each day.

This is an investigational study. The proton beam machine used to deliver treatment is approved by the FDA for patient use. The doses being studied are experimental. About 15 participants will take part in this study. All will be enrolled at MDACC.

Inclusion Criteria:

1. Pathologically confirmed chordoma of the skull base
2. Contrast enhanced postoperative MRI (CT in case MRI is contraindicated) of the skull base obtained within 90 days of study registration
3. MDACC surgeons have determined that optimal debulking of disease has been performed.
4. Karnofsky Performance status greater than or equal to 60
5. Signed informed consent

Exclusion Criteria:

1. Previous irradiation of the skull base
2. Documented evidence of disseminated metastatic disease
3. Any concurrent malignancy (other than non-melanoma skin cancers) in the last 3 years