Whole-comparative genomic hybridization (W-CGH) allows one to identify copy number differences in highly repeated DNAs between two genomes. It allowed the identification of nuclear markers that can be used to distinguish cell populations from different individuals in a chimeric situation. We discuss the reliability of W-CGH accomplished with fluorescent in situ hybridization (FISH) and digital image analysis (DIA) to analyze the degree of chimerism in patients after allogeneic hematopoietic stem cell transplantation (HSCT).