Aggressive angiomyxoma is a rare mesenchymal tumor occurring mainly in the vulvar region extending into the paravaginal and perirectal region. Histologically, this tumor is rich in vascular structures and in collagen fibers and is of myxoid appearance. Cytogenetic and molecular analysis was performed on a case of an aggressive angiomyxoma and revealed clonal karyotypic abnormalities. All 50 metaphases analyzed showed a translocation involving the chromosomal region 12q14-15. Chromosomal aberrations involving the breakpoint region 12q14-15 are frequently seen in a variety of other mesenchymal tumors as uterine leiomyomas, lipomas, hamartomas of the lung, liposarcomas, or hemangiopericytomas. Therefore, this breakpoint region seems to be the most frequent chromosomal abnormality associated with the initiation of human mesenchymal neoplasms. To narrow down the breakpoint region on a molecular level in the cells of the angiomyxoma we performed FISH analysis with different cosmid clones originating from a yeast artificial chromosome and cosmid contig overspanning parts of the region 12q14-15. We were able to narrow down the region to approximately 70-80 kb belonging to an area designated a multiple aberration region, because it also includes the breakpoints of leiomyomas, lipomas, and pleomorphic adenomas with 12q13-15 abnormalities. Our molecular and cytogenic data suggest that angiomyxomas or at least a subset of them molecularly belong to the benign group of mesenchymal tumors showing multiple aberration region involvement.