The study was aimed to investigate the origination of abnormal clones in hematopoietic cells of MDS patients. That is to say if there are abnormal clones in CD34(+)CD38(-) and CD34(+)CD38(+) cells and their proportions in MDS patients. Immuno-magnetic bead technique was used to sort CD34(+)CD38(-) and CD34(+)CD38(+) in bone marrow mononuclear cells of 9 MDS patients with chromosome abnormalities (four cases with trisomy 8, 1 case with trisomy 8 complex karyotype, 2 cases with 5q(-), 1 case with 5q(-)complex karyotype, 1 case with 5q(-) accompanying trisomy 8) and smears were made respectively. Then the percentage of abnormal clones in CD34(+)CD38(-) and CD34(+)CD38(+) cells were compared by using FISH. The results indicated that abnormal clones were involved in the two population cells in 9 patients. The percentage of abnormal clones in CD34(+)CD38(-) cells (41.8 ± 8.4%)was obviously lower than that in CD34(+)CD38(+) cells(72.4 ± 7.7%) (p < 0.001), and the percentage of abnormal clones in karyocytes was 70.8 ± 9.2%. It is concluded the abnormal clones of bone marrow hematopoietic cells may originate from stem cell stage in MDS patients with 5q(-) and +8, and the abnormal clones are predominant at stage of progenitors.