We describe here a unique case of therapy-related myelodysplastic syndrome (t-MDS) with inv(16)(p13q22) after autologous stem cell transplantation for lymphoma. The rare and smallest I type CBFbeta/MYH11 fusion transcript with a breakpoint at nucleotide 399 of CBFbeta and at nucleotide 2134 of MYH11 was detected in the bone marrow cells by reverse transcription polymerase chain reaction analysis. However, the fusion transcript was undetectable in the pretransplant peripheral blood stem cells. These results suggest that the stem cell damage leading to t-MDS may be induced mainly by the conditioning regimen for transplantation. Taken together with previous reports, the I type fusion transcript is preferentially induced with chemotherapy.