Genetic aberrations in cartilaginous tumors have not yet been well characterized. We analyzed the molecular-chromosomal aberrations in 10 chondrosarcomas (four Grade-3 tumors, four Grade-2 tumors and two Grade-1 tumors) and in three benign cartilaginous tumors (two enchondromas and one chondromyxoid fibroma). Genomic imbalances were detected in 9 out of 10 cases of chondrosarcomas. The median number of changes was 7.0 per tumor (range 0-23) and the gain-to-loss ratio was 1:1.4. The most frequent gains involved 7q, 5p, or 21q and the most frequent losses were 17p, 13q, 16p, or 22q. The three benign cartilaginous tumors each had two (0 gains and two losses), six (one gain and five losses) and eight (one gain and seven losses) chromosomal aberrations. Both of the gains occurred on 13q21 and losses were frequently observed on chromosomes 19 and 22q in all three cases. Loss of chromosomes 16p, 17p, 22q, or 19 loss were common in both chondrosarcomas and benign cartilaginous tumors. However, aberrations from chromosomes 2 to 11, 14, 15, 18, or 21 were detected only in chondrosarcomas. Therefore, although the number of aberrations between benign and malignant cartilaginous tumors appears to be similar, these two entities may be differentiated by determining which chromosomes are affected.