Aside from microscopically visible chromosomal rearrangements, numerous cryptic chromosomal alterations have been reported since the introduction of techniques like FISH, array-CGH or MLPA. This is especially true of dynamic regions in the subtelomere and subcentromere of any chromosome. To address these regions, locus-specific FISH probes are employed as single, chromosome-specific or genome-wide probe sets. Here we present the chromosome-specific subtelomere–subcentromere multicolor FISH (subCTM) and genome-wide subcentromere multicolor FISH (subcenM) probe sets, which are useful as screening tools in specific patient groups like the infertile and mentally retarded, as well as in tumor cytogenetics and for evolutionary studies when applied as ZOO-FISH.