Myelodysplastic Syndrome (MDS) cells present genetic instability and dysregulation of the gene C3ORF9, which was isolated from an MDS cDNA library and codes for a putative protein. We studied the expression of C3ORF9 in MDS syndromes to contribute to the understanding of the pathophysiology of MDS. One hundred and thirty-one patients and 35 healthy controls were involved in our study. Bone marrow aspirates and isolated CD34+ cells were used. Gene expression was estimated by quantitative PCR. C3ORF9 was found to be down-regulated in patients with CMML compared to the controls (p<0.01). There was no difference between RARS and the controls (p=0.1), while increased expression was found in RA, RAEB and RAEB-T (p<0.01 for all). No mutations or polymorphism were detected in our population. CD34+ cells expressed higher levels of C3ORF9 (p<0.01) in patients. The gene expression was correlated to the percentage of +cells in RAEB and RAEB-T (r=0.64). The altered C3ORF9 expression was possibly due to different gene regulation in these patients and/or to the increased CD34+ cells.