Here we report on the use of a new real-time polymerase chain reaction (PCR) method to detect and quantify the activating gene mutation of the tyrosine kinase JAK2. We evaluated patients with myelofibrosis with myeloid metaplasia (MMM; n=25) for the gene mutation prior to allogeneic stem cell transplantation and monitored them in the long-term follow up of 125 months (median 15, range 4-125) after transplant. The results obtained were correlated to the chimerism status of these patients. The JAK2 gene mutation was detected in 15 of 25 analyzed patients prior to transplant. Three patients who were again positive for JAK2 after transplant also had mixed chimerism status. These three patients relapsed from MMM shortly after JAK2 gene mutation was detected for the first time after transplant. Our presented data shows the feasibility of the detection of JAK2 gene mutation by real-time PCR as a minimal residual disease marker after transplant.