Copy number variants are a recently discovered source of large-scale genomic diversity present in all individuals. We capitalize on these inherent genomic differences, focusing on deletion polymorphisms, to develop informative fluorescence in situ hybridization probes with the ability to unequivocally distinguish between donor and recipient cells in situ. These probes are accurate, specific, highly polymorphic and, notably, can be used to assign genetic identity in situ in a completely gender-independent fashion. We anticipate that these polymorphic deletion probes will be useful in further understanding the dynamics of cellular chimerism after transplantation, including the details of chronic organ rejection, post-transplant lymphoproliferative disorder and graft-versus-host disease, and in optimizing future tissue engineering and pluripotent stem cell therapies.