Highly polymorphic tandemly repetitive DNA sequences provide powerful genetic markers for the identification of individuals by restriction fragment length polymorphisms (RFLP) even in close relatives. Over a three-year period, 61 consecutive patients from a single institution undergoing allogeneic bone marrow transplantation (BMT) for various hematological diseases were grafted with unmanipulated marrow and followed for the development of hematopoietic chimerism. Three synthetic oligonucleotide probes homologous to the so-called minisatellite or variable number of tandem repeat (VNTR) sequences were evaluated in the clinical setting of BMT for their usefulness: (i) to document marrow engraftment or rejection; (ii) to elucidate the kinetics of mixed chimerism; and (iii) in providing a sensitive tool for early detection of relapse. In addition, in patients with CML karyotyping and analysis of bcr/abl gene rearrangement was performed. Using this panel of three oligonucleotide probes, informative markers specific for donor or recipient RFLP could be demonstrated in all cases. Engraftment could be documented in all patients surviving beyond day +14 after BMT. Mixed chimerism was detected in 14% of the patients in the early phase (day +14 to day +78) after BMT but only one patient turned out to become a long-term stable mixed chimera. These results support the hypothesis that lymphocytes of recipient origin surviving the conditioning regimen may considerably contribute to mixed chimerism early after BMT. Long-term stable mixed chimerism is a rare event after BMT with unmanipulated marrow. Simultaneous analysis of chimerism after BMT by VNTR-RFLP, karyotyping, and detection of bcr/abl rearrangement in patients with CML showed corresponding results in nine out of 12 patients. In three patients either one of the methods failed to detect residual recipient cells in the early phase after BMT. Therefore different methods for assessment of mixed chimerism seem to complement rather than to exclude each other. Eleven patients who all exhibited complete chimerism early after BMT relapsed from their underlying disease. In seven of these patients grafted for acute leukemia, analysis of DNA-RFLP had been performed shortly before clinical relapse (30-86 days) and failed to herald relapse. As the sensitivity for the detection of the minor cell population by analysis of DNA-RFLPs is approximately 1%, these data may indicate that relapse of acute leukemia after BMT is characterized by a sudden increase in the percentage of recipient blast cells not detectable even by frequent RFLP analyses.