We analyzed the clinical course and risk factors of 18 patients with poor engraftment after allogeneic bone marrow transplantation (BMT), defined as absolute neutrophil count below 0.1 x 10(9)/l 28 days post-BMT. Significant risks associated with non-engraftment included HLA one antigen mismatch, BMT from matched unrelated donor, and a low dose of colony-forming units-granulocyte-macrophage (<10(4)/kg). Examined by a semiquantitative analysis of polymorphic microsatellite markers, donor DNA chimerism on day 28 was found to be predictive of treatment outcome. Seven patients had detectable donor DNA, varying from 43 to 100%. Five of them responded to granulocyte colony-stimulating factor (G-CSF) and achieved engraftment. Two were given further infusions of peripheral blood hematopoietic stem cells (PBSC) from the same donors, resulting in engraftment in one of them. Eleven patients had no detectable donor DNA, and none responded to G-CSF. Autologous regeneration occurred in six of these patients, four after infusion of backup marrow and two spontaneously. The remaining five patients died despite the administration of PBSC from the same or different donors. Regular monitoring of donor DNA chimerism is useful in the management of patients at high risk of poor engraftment.