Abstract An investigation of numerical and structural chromosome aberrations using chromosome arm-specific multicolor fluorescence in situ hybridization ( armFISH) revealed considerable genetic heterogeneity among and within 11 glioma cell lines. Despite the substantial variation in numerical chromosome alterations among the cell lines, several distinct and glioma growth-associated losses or gains were frequently observed, that is, losses of chromosomes 10, 13, and 22 and gain of chromosome 7 in particular. Structural aberrations frequently affected chromosomes 1, 4, 7, 16, and 19; however, no single structural chromosome aberration common to all or even several glioma cell lines could be found. Structural alterations were often multiform, and a large variety of unstable chromosome structures were detected. Two of the cell lines also harbored small marker chromosomes containing mainly heterochromatin and chromosomal insertions within hetero-chromatic regions. Altogether, the armFISH provides a versatile tool for the identification of chromosomal aberrations as well as their formation patterns in tumors with a complex genome at the level of chromosome arms.