A standardized chelation protocol was applied by stratifying transfusion-dependent thalassemic patients into three groups, namely well chelated group (A), inadequately chelated group without (B) or with (C) risk of cardiac complications based on serum ferritin (SF) levels and magnetic resonance imaging (MRI) cardiac T2* measurements. Group A patients were advised to continue with deferoxamine (DFO) (Regimen Ic). Group B patients were given options of either intensification of DFO alone (Regimen Ii), deferiprone (L1) alone (Regimen II) or combined therapy with L1 and DFO (Regimen III). Group C patients were advised to take either Regimen Ii or Regimen III. The 1-year result showed that the combined therapy (Regimen III) significantly reduced SF level, cardiac and liver iron in the groups of inadequately chelated patients. The same set of outcome parameters was repeated at 2.5 years of treatment so as to evaluate the intermediate-term effects of this risk stratified chelation protocol. The number of patients with cardiac T2* <20 ms decreased from 34 (60%) at baseline to 17 (30%) of the whole cohort of 57 patients at the end of the study. There were further improvements in SF, cardiac and liver T2* in Group C patients. Significant improvement in left ventricular ejection fraction (LVEF) was demonstrated after 2.5 years of the combined therapy group in which the change was not initially apparent after the first year of assessment.