In addition to its established hematological indications, autologous hematopoietic SCT (HSCT) can ameliorate the course of severe autoimmune disorders through a reconditioning of the immune system. We have shown earlier that HSCT determines extensive renewal of the TCR repertoire in multiple sclerosis patients. However, the observed persistence post-therapy of some pre-existing T-cell clones suggested the potential for disease recapitulation. Here, we investigated whether TCRs that reappear after a myeloablative conditioning regimen and HSCT were reintroduced with the autologous, CD34-selected hematopoietic stem cell (HSC) graft. In all, we cloned and sequenced 2237 TCR clones from peripheral blood and HSC grafts from four patients who underwent autologous HSCT for severe multiple sclerosis. Surprisingly, in-frame TCR sequences were detectable in only one of four patient grafts and no TCR sequences were found to be shared between the graft and pre-or post-HSCT samples. These findings provide the first evidence from extensive sequencing analysis to suggest that T cells in autologous HSC grafts that have been mobilized with CY+ G-CSF and CD34-selected have limited survival capacity and are therefore unlikely to be a major source of carryover of T-cell expansions potentially involved in autoimmune disease.