No curative treatment exists for patients with myelodysplastic syndrome (MDS) besides allogeneic stem cell transplantation. Hence, palliative treatment is provided for a life time accruing high health care cost. As no study in cost of MDS exists in Germany, the objective of this study was to assess and analyze costs of transfusion-dependent low/intermediate-1-risk MDS in Germany from a payers' perspective. From seven centers, 116 low/intermediate-1-risk transfusion-dependent MDS patients with and without isolated 5q-deletion were identified. Claims data and patient records of the previous 5 years were used to collect health care utilization data retrospectively. Publicly available tariff books and remuneration schemes were applied to evaluate mean costs per year in Euro with 2007 as base year. The annual cost of MDS patients was estimated at <euro>14,883. Subgroup analyses showed differences in patient's characteristics and outcomes among patients treated at a hospital-based vs. an office-based setting. Patients treated at the hospital-based registry show higher cost, whereas the reasons for that still need to be detected. Overall, per annum direct costs range from <euro>12,543 (SD 12,967) to <euro>24,957 (SD 36,399) in different subgroups of patients. In both groups, patients with 5q-deletion use more medication than those without deletion. Mean costs for medication in the office-based setting are <euro>5,902 for patients with isolated 5q-deletion vs. <euro>3,932 for patients with no deletion, respectively. MDS leads to a high health care utilization and resulting costs for the health care system which requires a detailed analysis of underlying services.