Atypical lipomatous tumor (ALT), an intermediate malignant neoplasm of soft tissues, is characterized by the presence of supernumerary ring and giant marker chromosomes. These supernumerary chromosomes consistently contain amplified 12q-material in association with amplified segments from a variety of other chromosomes. However, a few cases of ALT with other types of chromosomal rearrangements have been reported earlier. We report on new types of structural aberrations in a case of ALT. In a pseudodiploid karyotype, there were two aberrant chromosomes, both consisting of alternating chromosome 8 and 12 sequences as shown by multicolor fluorescence in situ hybridization (FISH). The complex rearrangement was not only the result of multiple breaks and reunions of these chromosomes, but was also associated with a gain of chromosome 12 sequences. FISH analyses revealed that the number of MDM2 signals was slightly elevated (median, 5). There were three intact copies of HMGA2 and one additional copy of the 5' part of the gene. These findings are consistent with previous reports that the ALT phenotype may be associated with a low or moderate level of gene amplification, whereas truncation of HMGA2 has been observed in both ALTs and benign lipomas. The aberrations in the present case were stable, although rare cells with higher MDM2 copy numbers were detected. Whether ALTs with these types of aberrations have a lower risk of tumor progression than ALTs with the notoriously mitotically unstable ring and giant marker chromosomes remains to be investigated.