Bone marrow transplantation (BMT) is a therapeutic process used to treat a variety of hematologic diseases. After BMT, the documentation of engrafting with the use of genetic markers is obligatory. C-band polymorphism is an excellent genetic marker because it occurs with high frequency in all populations studied and shows a high stability in vitro and in vivo. We studied a total of 36 patients: 15 with myeloid leukemia and 21 with severe aplastic anemia (SAA), submitted to BMT. The majority of the patients with chronic granulocyte leukemia (CGL; 10/15, 67%) and with SAA (17/21, 81%) showed a frequency of host cells around 15% (CGL) and 8% (SAA) in the first period analyzed (day +30 post-BMT); with a decrease in the others (+90, +180 to CGL and SAA and +365 only to CGL). In our study, the persistence of host cells in these proportions did not imply an unfavorable prognosis. On the contrary, some patients with myeloid leukemia (5/15 33%) and SAA (4/21, 19%) showed high proportions of host cells in one or more periods analyzed. If compared to the first group, these patients had, in general, a poor clinical evolution, with rejections, relapses, and deaths in greater numbers. These results show the important contribution of cytogenetic analysis in the follow-up of patients submitted to BMT.