Abstract: Objectives To study the changes of clonality of T cell receptor (TCR) and complementarity determinative region 3(CDR3) before and after autologous peripheral blood CD34+ stem cell transplantation(auto-PBSCT) for severe/refractory connective tissue disease（CTD）. Methods Thirteen patients with severe/refractory CTD were enrolled for auto-PBSCT in Peking Union Medical College Hospital, including systemic lupus erythematosus (SLE) 8 cases, rheumatoid arthritis(RA) 4 cases, and primary Sjogren's Syndrome( pSS) 1 case. Blood samples were collected before/after mobilization, 2 weeks, 1 month, 3 months , 6 months 12 months 18 months post-transplantation. Diversity of TCR BV and CDR3 were showed by reverse transcription- polymerase chain reaction( RT-PCR) and genescan. Rusualts The TCR BV usage and CDR3 spectral pattern of pre-auto-PBSCT CTD patients were revealed skewed pattern and oligoclonality, Which developed severe oligoclonality within 1 months after auto-PBSCT. However, they showed diversity and poly-clonality 3-6 months after auto-PBSCT. Conclusion Skewed pattern and oligoclonality of TCR BV and CDR3 which implied auto-reactive were depressed after auto-PBSCT, and inclined to change to normal pattern.