Chordoma is a rare neoplasm arising in the cerebrospinal axis from nothochordal remnants. The commonest location is in the sacrococcygeal area, then in the sphenooccipital region and less frequently in other parts of the vertebral column. Chordoma has been found in all age groups, but the greatest incidence was found between the fifth and the seventh decades: there is a male predominance. Signs and symptoms of chordoma are related to tumor location and are often present for a long period of time because of the slow growth of the neoplasia. Sacrococcygeal chordomas may produce lower back pain, bladder or anorectal dysfunction or mass. Three histologic subtypes are currently considered: conventional, chondroid and dedifferentiated chordoma. Comparing with conventional chordoma, chondroid chordoma shows a better prognosis while dedifferentiated chordoma has a worse prognosis. However the malignant potential of chordoma is most likely due to incomplete surgical excision because of the multifocality of the neoplastic growth. For that reason, local recurrence is common and accounts in large part for the mortality for this tumor. The best treatment consists of a wide surgical excision coupled with adjuvant radiation therapy. We report a case of sacrococcygeal chordoma arised in a 48 year-old-man; the clinical features of the tumor showed a close resemblance with a pilonidal cyst. When the diagnosis of conventional chordoma was done the patient were treated by surgery and by intraoperative radiotherapy followed by external radiotherapy. This peculiar therapy was adopted in the attempt to reduce the risk of local recurrence. Six months after this treatment the patient was well and no signs of local recurrence was found by the magnetic resonance imaging.