We have used OmniPlex library technology to construct chromosome painting probes from single copies of flow sorted chromosomes. We show that this whole genome amplification technology is particularly efficient at amplifying single copies of chromosomes for the production of paints and that single aberrant chromosomes can be analysed in this way using reverse chromosome painting. The efficient generation of painting probes from single copies of sorted chromosomes has the advantage that the probe must be specific for the chromosome sorted and will not suffer from contamination from other chromosomes particularly in situations where flow karyotype peaks are poorly resolved. These initial results suggest that OmniPlex whole genome amplification will be equally effective in other cytogenetic applications where only small amounts of DNA are available, i.e. from single cells or from small pieces of microdissected tissue.