Chordoma is an uncommon malignant neoplasm derived from remnants of the embryonal notochord. The tumor arises in the sacrococcygeal region in most cases. Cytogenetic information on clival chordomas is scarce due to the low incidence of these tumors. In this study, we applied the G-banding and spectral karyotyping techniques to compare the karyotypes of three variants of clival chordoma: conventional, chondroid, and dedifferentiated. We describe a normal karyotype of a chondroid chordoma and a complex karyotype of a conventional chordoma involving chromosomes 1, 2, 3, 5, 8, 9, 11, 15, 19, 20, and X. The cytogenetic analysis of the dedifferentiated chordoma showed a polyploid complex karyotype of 71-123 chromosomes with double minutes that originated from chromosome 17.