Development of further diagnostic and prognostic tools in myelodysplastic syndromes (MDS) is warranted. In this study we tested two molecular markers in bone marrow of MDS patients: Galpha16, a hematopoiesis-specific G protein alpha subunit serving as an intracellular marker of hematopoietic activity, and 5'-lipoxygenase (5-LO), a putative differentiation marker. The results were correlated with clinical and laboratory features and outcome. Bone marrow mononuclear cells were evaluated by block cycler PCR in 32 patients for Galpha16 and in 25 patients for 5-LO. In 12 patients cDNA analyzed by the block cycler method was quantified by real-time quantitative (RTQ) PCR for both Galpha16 and 5-LO. The results confirmed concordance of the two methods. All FAB and WHO subtypes were positive for at least one of the two genes. Strikingly, only 1 of 11 patients with refractory anemia with ringed sideroblasts was positive for Galpha16. No correlation between Galpha16 or 5-LO and bone marrow cellularity or cytogenetic risk factors (IPSS) was detected. Only combined evaluation of Galpha16 and 5-LO expression showed a correlation with extent of anemia and thrombocytopenia. A relationship between the two markers and preleukemic duration was found. Our findings show that both Galpha16 and 5-LO can be expressed in MDS, reflecting proliferation and differentiation processes in this disease. Different expression patterns of the two molecules indicate that proliferation and differentiation of hematopoietic cells may occur independently. These parameters could constitute a new class of risk factors in MDS. Determination of Galpha16 and 5-LO expression may provide a tool for observing growth and maturation in these diseases.