Monosomy 7 is the most frequent chromosome abnormality among patients with secondary myelodysplastic syndrome (MDS). We used fluorescence in situ hybridization (FISH) and fluorescence-activated cell sorting (FACS) in order to clarify the lineage involvement. Four patients, three with de novo MDS and one with secondary MDS, were enrolled in this study. Monosomy 7 was observed in pluripotent stem cells (CD34(+)Thy-1(+)), and in B (CD34(+)CD19(+)) and T/natural killer (NK) progenitors (CD34(+)CD7(+)). The number of abnormal cells of B (CD19(+)) and T (CD3(+)) cells was below the cut-off value, but approximately 60% of the NK cells (CD3-CD56(+)) contained monosomy 7 in three of the patients.