Chordoma is a rare, low- to intermediate-grade malignant tumor involving the axial spine. Cytogenetic data on these tumors have been limited to 25 cases. The findings of clonal chromosome aberrations in five new cases are presented. One of these and two previously reported cases have been studied with multicolor combined binary ratio labeling fluorescence in situ hybridization (COBRA-FISH). The karyotypes were near-diploid, mostly with several numerical and structural aberrations. There were multiple imbalances, with loss of segments from 1p, 3p, 3q, 9p, and chromosome 10 seen in two to four of the seven cases. No clustering of breakpoints was seen and no recurrent recombination between chromosomes was detected. The findings are consistent with previous data and indicate that chordoma tumor development is associated with multiple, nonrandom losses including chromosome segments that are frequently involved in many other solid tumors.