Within the last few years, the first peptide vaccination trials for treatment of acute myeloid leukemia (AML) have been initiated. Athough the presence of epitope-specific T cells could be seen both in bone marrow (BM) and peripheral blood (PB), nothing is known about their clonal composition. In this study, we analyzed material from a patient with recurrent AML vaccinated with "Wilms Tumor Protein 1" (WT1) peptide, who achieved a complete remission (CR) lasting for 12 months. For identification of expanded WT1-specific T-cell clones, enrichment by tetramer and IFNγ secretion were followed by comparative quantitative reverse transcribed PCR (qRT PCR) quantification of all TCR Vβ-families. Vβ-families with increase in the enriched fraction were cloned and sequenced. A predominant clone was quantified by clonotypic qRT PCR from PB and BM. Quantity and functionality of WT1-specific cells were assessed by tetramer analyses and intracellular IFNγ staining. A specific predominant clone was identified during clinical remission. Clone-specific qRT PCR showed an increase both in PB and BM after 8 vaccinations. Six months after achieving CR, the transcript levels in BM decreased. Relapse was accompanied by secondary rise of the WT1-specific clone in PB but not in BM. In parallel, a lack of vaccine-induced WT1 specific IFNγ production was observed at that timepoint. In conclusion, we provide first data regarding evolution and compartmentalization of a peptide vaccine-induced T-cell clone in PB and BM of an AML patient. At the time of relapse, the same clone reappeared spontaneously in PB but not in BM showing impaired functionality.