Hematopoietic stem cell transplantation (HSCT) is an effective, but invasive, treatment that is increasingly applied for a variety of cancers and congenital immunodeficiency disorders. It has shown promising, durable responses in some patients, but remains a dangerous procedure with many potentially life-threatening complications. Assessment of the TCR repertoire in HSCT recipients has shown to provide crucial information required to improve patient care. Spectratyping, currently the gold standard for TCR repertoire assessment, is notably limited by its resolution and unable to provide data on the nucleotide level. The application of repertoire sequencing can provide novel insights into immune recovery in these patients and help us to better understand clonotype dynamics during clinically relevant events, such as infections, oncologic relapses and graft-versus-host disease.