To date, there have been few studies published on benign and malignant cartilage tumours using high resolution molecular cytogenetic techniques such as spectral karyotyping (SKY). In this study we have used a combination of chromosome banding, SKY and FISH to characterize the chromosomal pattern in 18 benign and malignant cartilage tumours and one small cell osteosarcoma with mesenchymal chondrosarcoma-like features. Clonal structural and/or numerical aberrations were detected in 14 of these tumours. All chondroblastomas and the chondromyxoid fibroma had diploid or near-diploid karyotypes with often relatively simple karyotypes. Although no consistent abnormalities were detected in the chondroblastomas, recurrent breakpoints were found at 2q35, 3q21-23, and 18q21. The chondromyxoid fibroma had an inv(6)(p25q13) as the sole anomaly, suggesting that this is a primary abnormality characteristic of this entity. The karyotypic findings in the chondrosarcomas were, as a rule, more complex than those in the benign tumours. A typical feature was the frequent occurrence of unbalanced rearrangements leading to genomic imbalances with losses and gains of certain chromosomes or chromosome regions. The following breakpoints were recurrent: Xq21, 6p10, 9p13, 20p11 and 22q11-12. Despite the use of high-resolution molecular cytogenetic techniques, we were not able to identify any consistent abnormalities in chondrosarcomas, suggesting that tumour-specific chromosome changes are not likely to be found in this group of tumours.