BACKGROUND: We analyzed T cell receptor beta chain (TCRB) gene to investigate the presence of putative T cell clones and its clinicopathologic implications in Korean patients with aplastic anemia (AA). METHODS: Twenty-nine bone marrow specimens were collected from 20 AA patients, 19 specimens from initial diagnosis and 10 from follow-up. T cell clonality assay was performed using IdentiClone(TM) TCRB Gene Clonality Assay kit (InVivoScirbe Technology, USA) and automatic genetic analyzer. Patients' clinical information and laboratory parameters were also analyzed. RESULTS: Five patients had definitive underlying factors related with aplastic anemia, such as hepatitis B virus (4 cases) and benzene exposure (1 case). Putative T cell clones were detected in bone marrow specimens of 11 (58%) out of 19 patients at diagnosis. The location of putative T cell clones of TCRB gene (diversity region, Dbeta; joining region, Jbeta; variable region, Vbeta) was distributed in Dbeta2+Jbeta2 (6 cases), Dbeta1+Jbeta1 (3 cases), Vbeta+Jbeta1 (2 cases), and Dbeta1+Jbeta2 (2 cases). Interestingly, among seven patients who underwent stem cell transplantation, five patients with no T cell clones detected at diagnosis developed new T cell clones during the follow-up. CONCLUSIONS: Putative pathogenetic T cell clones were detected in most of AA patients in the current study. T cell clonality assay would be useful for investigating the pathophysiology of acquired AA.