We report on a patient with a clinically diagnosed Philadelphia negative chronic myelogenous leukemia (CML) with a so far unrecorded complex translocation event between the two homologue chromosomes 5. At the GTG-band level the karyotype was normal, apart from an enlarged chromosome 5 and an extremely shortened second chromosome 5. Both derivative chromosomes 5 consisted exclusively of #5 derived material as proven by 24-color FISH. To characterize the complex aberration in more detail the multicolor banding (MCB) technique using a chromosome 5 specific probe set was applied. Using this DNA-based high resolution banding procedure, the karyotype could be described as 46,XX,del(5)(pterright curved arrow q12::q33right curved arrow qter),ins(5)(pterright curved arrow q15::q12right curved arrow q21::q21right curved arrow qter). In consequence, the aberration leads to a partial deletion of the long arm of chromosome 5: del(5)(q21q33), which would not have been identified using conventional banding techniques or 24-color FISH.