Distinguishing between host and donor origin of cells after bone marrow transplantation is important in understanding the engraftment process. Restriction fragment-length polymorphism (RFLP) analysis, the most generally applicable approach for this purpose, is limited by a requirement for at least 10(6) cells per assay. The small number of cells available at early time points post-BMT has thus precluded studies of early engraftment kinetics. This report describes the application of the polymerase chain reaction (PCR) to engraftment analysis following allogeneic BMT. We describe a series of PCR polymorphisms (PCRFLP/s) that allows the distinction of most patient-donor pairs (excluding identical twins). Thirteen patient-donor pairs were evaluated using this approach, and engraftment data obtained at time points when leukocyte counts were often too low for conventional analysis. This approach is quantitative and significantly more rapid than conventional techniques. (Analysis can be completed in less than a day). Serial evaluation at early time points post-BMT in five patients demonstrated residual host cells early (days 7-14) followed by their subsequent rapid disappearance. In one patient an apparent resurgence of host elements occurred around days 28-35, followed by a sharp decline by day 42.