Hypomethylating agents such as 5-azacytidine or decitabine have been a major breakthrough in the treatment of patients with myelodysplastic syndromes (MDS). They have been shown to improve transfusion requirements and change the natural history of the disease. However, with increasing cumulative clinical experience, it has become apparent that these agents are not curative and have their own shortcomings. There are a subgroup of patients who do not respond to frontline therapy and a large, growing cohort of patients that lose response or progress while on hypomethylating agent-based therapy. There are no standard treatment options in this arena and is therefore a focus of significant research interest. Since the mechanisms of resistance to hypomethylating agents are not known, selection of therapy is largely empiric, but must take into account the age, comorbidities, and performance status of the patient as well as the characteristics of the disease at the time treatment failure. Higher intensity approaches and allogeneic stem cell transplant can yield high response rates and long term disease control, but should be limited to a selected cohort of patients who can tolerate the treatment related morbidities. For the majority of patients who will likely be better candidates for lower intensity therapy, several novel, investigational approaches are becoming available. Among these include newer nucleoside analogues, inhibitors of protein tyrosine kinases, molecules that interact with redox signaling within the cell, immunotherapy approaches, and others. Patients with MDS whose disease has failed hypomethylating agent therapy should be referred for clinical trials when available. As we learn more about the patterns and mechanisms of failure, the next challenge will be determining which therapies would be suitable for each individual patient.