Therapeutic decisions in patients with myelodysplastic syndromes (MDS) are very complex. The dilemma that confronts the management of MDS is illustrated by the presence of only one agent (5-azacitidine), which has been approved by the U.S.A. Food and Drug Administration, with an indication for all subtypes of this disease and another one (lenalidomide) for the management of a specific MDS subgroup, the 5q-syndrome. Current classifications and prognostic systems do not take into account the considerable clinical heterogeneity of MDS or their diverse biology. Supportive care, low-intensity treatment, acute myeloid leukemia-type therapy, and stem cell transplantation (SCT) produce unsatisfactory results because patients continue to be exposed to the inherent complications of worsening cytopenias and leukemic transformation. Recent years have witnessed an evolution in our understanding of pathophysiology pathways in MDS. At the same time, many novel and targeted therapies are being investigated in clinical trials, offering patients the prospect of sustained benefit and changing the natural course of the disease. Hypomethylating agents, immunomodulatory drugs, and farnesyl-tranferase inhibitors have produced very promising results in terms of response and survival in MDS patients. This review summarizes all recent data on the role of novel agents and SCT in the treatment of patients with MDS in an attempt to better understand their possible therapeutic status in the management of these patients.