Engraftment following allogeneic bone marrow transplantation (BMT) was assessed in three cases, two of which were sex-mismatched and one sex-matched. The polymerase chain reaction (PCR) was used to amplify the hypervariable region lying 3' to the apolipoprotein B gene on chromosome 2. Amplification of this region provided informative marker bands capable of distinguishing host/donor populations in each case. The method allowed rapid analysis of minimal numbers of cells from peripheral blood and bone marrow in the early stages following BMT and was predictive of either successful engraftment or graft failure.