AbstractDeletions and structural rearrangements of the long arm of chromosome 13 are frequently observed in benign and low‐malignant lipomatous tumors, but nothing is known about their molecular genetic consequences. We assessed the karyotypes of 40 new and 22 previously published cases (35 ordinary lipomas, 15 spindle cell/pleomorphic lipomas, 2 myxolipomas, 1 angiomyxolipoma and 9 atypical lipomatous tumors) with chromosome 13‐abnormalities, and found bands 13q12–22 to be frequently affected. Twenty‐seven cases with structural abnormalities within this region were selected for breakpoint and deletion mapping by metaphase fluorescencein situhybridization (FISH), using a set of 20 probes. Deletions were found in 23 of 27 cases. The remaining 4 cases had seemingly balanced rearrangements. The breakpoints were scattered but clustered to band 13q14, and in all cases with unbalanced abnormalities, a limited region within band 13q14 was partially or completely deleted. A deletion within band 13q14 was found together with a breakpoint on the other homologue in 5 cases, 4 of which could be tested further with regard to the status of the retinoblastoma (RB1)‐gene. In all 4 cases, only 1 copy of the gene was deleted. In addition to the breaks and deletions in the vicinity of theRB1‐locus, several other regions of 13q were recurrently affected,e.g., in the vicinity of the hereditary breast cancer (BRCA2; 13q12)‐ and lipoma HMGIC fusion partner (LHFP; 13q13)‐ genes. Our findings strongly indicate that deletion of a limited region (∼2.5 Mbp) within 13q14, distal to theRB1‐locus, is of importance in the development of a subset of lipomatous tumors. © 2002 Wiley‐Liss, Inc.