In patients with myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML), expression of the hematopoietic stem cell marker CD34 has been associated with a poorer prognosis. CD34 is usually analyzed by flow cytometry (FC), but may also be analyzed using immunohistochemistry (IH). The present study was undertaken to compare these 2 methods. Bone marrow from 16 patients with MDS and 12 with AML and from 12 healthy young volunteers was studied. The expression of CD34 was analyzed with FC on fresh bone marrow cells and with IH on sections of paraffin-embedded bone marrow. The correlation between FC and IH was good both for patients with MDS (p<0.0001) and AML (p<0.01). However, in patients with a high number of CD34-positive cells, the FC method seemed to result in a higher percentage of positive cells compared to the IH method. In normal bone marrow, the ratio between the percentage of CD34-positive cells and the percentage of bone marrow blasts was approximately 0.8. In the whole group of MDS patients, this ratio was 1:1, while in patients with refractory anemia (RA) and ring sideroblastic anemia (RAS) it was 1.6. Patients with MDS differed significantly from patients with de novo AML, who showed a ratio of only 0.23 (p<0.01). We conclude that the FC and IH methods for measuring expression of CD34 are well-correlated in MDS and reasonably well correlated in AML. A stem cell phenotype is more commonly expressed on precursor cells from patients with MDS than from patients with AML.