In this retrospective study, 209 patients with malignant disease were analyzed for levels of T-cell receptor excision circles (TRECs) for the first 24 months after allogeneic stem cell transplantation. CD3+ cells were separated by direct antibody-coupled magnetic beads, followed by DNA extraction according to a standard protocol. The δRec-ψJα signal joint TREC was measured with real-time quantitative PCR. Patients were grouped based on malignant disease; Chronic myeloid leukemia (CML), chronic lymphatic leukemia (CLL), acute myeloid leukemia (AML), acute lymphocytic leukemia (ALL) and myelodysplastic syndrome (MDS). Patients were further subdivided based on TREC levels below (low-TREC) or above (high-TREC) median at each time point. TREC levels were then correlated to relapse-incidence and relapse-free survival (RFS). For patients with AML, low TREC levels 2 months post-transplantation were correlated to high relapse incidence at 5 years (p=0,038). In patients with chronic leukemia high TREC levels were correlated with improved RFS (p=0.048). For patients with MDS, high TREC levels at 9 months post-transplantation were associated with higher RFS at 5 years (p=0.01) and lower relapse incidence (p=0.01). This study shows the potential use of TREC measurement in blood to predict relapse in patients with AML and MDS after ASCT.