Heat shock proteins (HSPs) are molecular chaperones involved in binding and regulating the levels of several client cellular proteins. HSPs are induced by stress and play a role in the modulation of apoptosis and proliferation. Expression of HSPs by acute myeloid leukemia (AML) cells has been reported to correlate with more aggressive disease. Here we used a flow cytometry approach to quantify the expression of HSP90 and HSP70 in specific cell populations in bone marrow. Quantification using QuantiBRITE and PE (phycoerythrin)-labeled antibodies with a 1:1 ratio allowed us to specifically measure the antibody binding capacity in 100 CD34+ cells (molecules/100 CD34+ or CD3+ cells). Using this approach, we compared bone marrow samples from patients with myelodysplastic syndrome (MDS) and patients with AML. This approach can also be used to monitor patients treated with therapeutic agents that target HSPs, such as 17-allylamino-17-demethoxygeldamycin (17AAG). The percentage of CD34+ cells expressing HSP90 (P=0.008) and HSP70 (P<0.001) was significantly lower in MDS (n=20) than in AML (n=33) patients. Similarly, the percentage of CD3+ cells expressing HSP90 and HSP70 was significantly higher in MDS than in AML patients (P<0.01). This suggests that the environment in the bone marrow (cytokines, chemokines, other factors) may affect the levels of HSPs in neoplastic and normal cells in a similar fashion. In patients with MDS, higher levels of HSP90 were associated with shorter survival (P=0.03). However, after achieving remission (CR), MDS patients who expressed high levels of HSP90 had significantly longer remission duration (CRD) (P=0.03). These findings not only confirm that the environment and blasts in patients with MDS are different from those in patients with AML, but also suggest that therapy targeting HSPs may be a rational approach in patients with MDS.