It has been demonstrated that 24-color FISH is not sufficient to understand completely the behaviour of chromosomal markers, especially in solid tumors. In the present study we show the usefulness of molecular cyto-genetic techniques, such as multicolour banding (MCB) and centromere-specific multicolour-FISH (cenM-FISH) performed on the colorectal cancer cell line SW480. Applying these approaches previously described chromosomal breakpoints could be redefined and six 'marker chromosomes' could be thoroughly characterised. Additionally, the cenM-FISH technique identified three stable dicentric chromosomes which have never been described before in SW480. In conclusion, here we present the first comprehensive characterisation of the complex karyotype of the colorectal cancer cell line SW480.