Adipose tissue tumors are often characterized by typical or even specific chromosomal alterations. In some of the cases the molecular background of these microscopically visible alterations was already elucidated. In myxoid liposarcomas the translocation t(12;16) creates a fusion gene between the CHOP gene and the FUS gene and in lipomas the HMGI-C gene becomes rearranged by structural aberrations involving chromosomal region 12q14-15. Based on examples of a lipoma, a well-differentiated liposarcoma, a myxoid liposarcoma, and an aggressive angiomyxoma it is demonstrated in the present paper how cytogenetic investigation can be used as an additional tool for an improved diagnosis of adipose tissue tumors. Furthermore, the detection of molecular mechanisms underlying the visible cytogenetic alterations will certainly significantly increase our knowledge about the pathogenesis of these diseases.