Background: Colorectal cancer (CRC) is the third most common cancer in human, and the fourth leading cause of death in adult men. Murine tumor cell lines have been established as model systems for CRC, but their cytogenetic properties have yet to be fully understood. Methods: The two murine colon-tumor cell lines, CMT-93 and CT26 (also called CT26.WT, CT-26 or CT-26 WT), were investigated in this study using molecular cytogenetic methods, i.e., multicolor-fluorescence in situ hybridization (mFISH), murine multicolor banding (mcb), and array-based comparative genomic hybridization (aCGH). The chromosomal imbalances and breakpoints characterized by these methods were compared with those of human CRCs using an in-silico-translation of murine data into the human genome. Results: CMT-93 and CT26 expressed a hyperdiploid and hypertriploid karyotype, respectively. While only clonal aberrations of chromosomes 2, 5, 8, and X were observed for CMT-93, there was greater variability of chromosomal imbalances observed in CT26. Both cell lines tended to form dicentric and neocentric chromosomes and showed 17 (CMT-93) and 28 tumor-associated breakpoints (CT26), respectively. Interestingly, the imbalances found were almost exclusively gains in somatic chromosomes. In addition, the Ychromosome was lost in CMT-93, as was one of the X-chromosomes in CT26. In-silico translation of the in both cell lines observed chromosomal imbalances showed a high agreement with the most frequently observed metastatic amplifications in human CRCs. Conclusions: The findings of our study revealed that murine tumor cell lines CMT-93 and CT26 are models for human CRCs of advanced-stage tumors. The information gained here is imperative for the application of CMT-93 and CT26 for future research in CRC.