The breast cancer cell line MCF-7 is a widely used model in breast cancer research however a number of conflicting reports have been published regarding its biological properties. We hypothesised that there will be significant in vitro mutation and genotypic evolution over time in this cell line. To assess the genetic divergence of MCF-7 at the chromosomal level, we analysed MCF-7 cell lines grown independently at three different laboratories using M-FISH and CGH. In addition, MCF-7 cells from our own laboratory were also analysed at two time points 18 months apart. Several common chromosomal translocations were identified in all variants of the cell lines. In addition, a significant number of unique abnormalities were identified, characterising each of the variants studied. Genotypic differences between cell lines grown independently in different laboratories would significantly alter the phenotypic characteristics of each cell line rendering biological properties inconsistent between laboratories.