To ascertain the clinical factors involved in T-cell reconstitution after allogeneic stem cell transplantation (SCT), we evaluated serial assessments of lymphocyte subsets by flow cytometry and TRECs levels by quantitative PCR in 83 adult patients. Patient age >25 years, unrelated donor, CMV infection and acute graft-versus-host disease (GVHD) adversely affected CD3(+) and CD8(+) T-cell recovery after SCT (p < 0.05). TRECs were low or undetectable during the first months after transplant and progressively increased thereafter. However, median TRECs of patients did never achieve normal values compared to healthy donors (median follow-up 9 months, range 2-42). Presence and severity of chronic GVHD significantly affected TRECs counts: patients with chronic GVHD had lower TRECs than patients without GVHD at 9, 12 and 24 months after SCT (p = 0.002, p = 0.022, p = 0.015). Patients with limited chronic GVHD had higher TRECs compared to patients with extensive GVHD (p = 0.018). No relationship was observed between fungal or bacterial infections and TRECs. Nonetheless, CMV infection was associated with lower TRECs (p = 0.032). Our data support the concept that adult thymus contributes with a slow but continuous production of thymic T cells to immune reconstitution after SCT. Chronic GVHD is the main factor associated to a delay in TRECs counts recovery.