The study evaluated the dynamics of microchimerism after allogeneic hematopoietic stem cell transplantation (allo-HSCT) in 18 patients with hematological diseases who underwent an enhanced dual conditioning (EDCT) regimen. Complete donor chimerism (CDC) was achieved in 16 patients (88.9%) at a median of 14 days after transplantation. Neutrophil and platelet engraftment occurred in a median of 15 and 25 days, respectively. Patients with constant CDC had faster platelet engraftment (19.5 vs. 40 days) and better overall survival (median OS not reached vs. 5 months, P = 0.015). The dynamics of microchimerism differed according to the type of transplantation; patients after peripheral blood transplantation (PBSCT) had shorter neutrophil and platelet engraftment times compared with cord blood transplantation (CBT), but final CDC rates and survival were not significantly different. The results suggest that microchimerism monitoring may be clinically useful for early intervention and treatment adaptation after allo-HSCT. This regimen and monitoring approach show promising long-term results in patients with hematological diseases.