The use of DNA markers known as restriction fragment length polymorphisms is a sensitive and informative method of distinguishing patient and allogeneic donor cells after bone marrow transplantation. To apply the test, it is necessary in each case to find DNA probes that display patient-specific and donor-specific bands in Southern transfer hybridization. We have isolated a set of 12 cloned DNAs from highly polymorphic loci by which siblings can usually be distinguished. With just four of these probes, we can expect to distinguish the genotypes of the recipient and a sibling donor in more than 99% of cases (except between identical twins). The availability of many highly polymorphic probes also allows selection of an optimal probe for each case, one that can detect both the patient and donor-specific bands in a single hybridization with maximum resolution and sensitivity. We have applied these probes to the analysis of cells from peripheral blood and bone marrow after transplantation and demonstrated their usefulness in confirming engraftment of donor cells or graft rejection, and in detecting mixed lympho-hematopoietic chimerism.