Assessment of the host immune status is becoming a key issue in allogeneic hematopoietic stem cell transplantation (allo‐HSCT). In the long‐term follow‐up of these patients, severe post‐transplant infections, relapse or secondary malignancies may be directly related to persistent immune defects. In allo‐HSCT, T‐cell differentiation of donor progenitors within the recipient thymus is required to generate naive recent T‐cell emigrants (RTE). These cells account for a durable T‐cell reconstitution, generating a diverse T‐cell receptor (TCR) repertoire and robust response to infections. It is now possible to quantify the production of RTE by measuring thymic T‐cell receptor excision circles or ‘TREC’ which are small circular DNA produced during the recombination of the genomic segments encoding the TCR alpha chain. Here we discuss the role of thymic function in allo‐HSCT. The pre‐transplant recipient thymic function correlates with clinical outcome in terms of survival and occurrence of severe infections. Post‐transplant, TREC analysis showed that the thymus is a sensitive target to the allogeneic acute graft‐versus‐host disease (GvHD) reaction but is also prone to recovery in young adult patients. In all, thymus is a key player for the quality of immune reconstitution and clinical outcome after allo‐HSCT. Thymic tissue is plastic and it is a future challenge to halt or reverse thymic GVHD therapeutically by acting at the level of T‐cell progenitors generation, thymic homing and/or epithelial thymic tissue preservation.