Delayed T cell recovery and restricted T cell receptor (TCR) diversity after allogeneic hematopoietic stem cell transplantation (allo-HSCT) are associated with increased risks of infection and cancer relapse. Technical challenges have limited faithful measurement of TCR diversity after allo-HSCT. Here we combined 5′ rapid amplification of complementary DNA ends PCR with deep sequencing to quantify TCR diversity in 28 recipients of allo-HSCT using a single oligonucleotide pair. Analysis of duplicate blood samples confirmed that we accurately determined the frequency of individual TCRs. After 6 months, cord blood–graft recipients approximated the TCR diversity of healthy individuals, whereas recipients of T cell–depleted peripheral-blood stem cell grafts had 28-fold and 14-fold lower CD4⁺ and CD8⁺ T cell diversities, respectively. After 12 months, these deficiencies had improved for the CD4⁺ but not the CD8⁺ T cell compartment. Overall, this method provides unprecedented views of T cell repertoire recovery after allo-HSCT and may identify patients at high risk of infection or relapse.