Chordoma of thoracic vertebras is a very rare locally invasive neoplasm with low grade malignancy arising from embryonic notochordal remnants. Radical surgery remains the cornerstone of the treatment. We describe a case of multifocal T1-T2 chordoma, without bone and disc involvement, incidentally misdiagnosed as a paraganglioma, occurring in a 47-year-old male asymptomatic patient. Neoplasm was radically removed by an endocrine surgeon through a right extended cervicotomy. A preoperative reliable diagnosis of chordoma, as in the reported case, is often difficult. Radical surgery can provide a favorable outcome but, given the high rates of local recurrence of this neoplasm, a strict and careful follow-up is recommended. Although very rare, chordoma should be suggested in the differential diagnosis of the paravertebral cervical masses of unknown origin. Spine surgeon consultation and a FNB should be routinely included in the multidisciplinary preoperative work-up of these neoplasms.