BACKGROUND: In some clinical situations, for which RCT are rare or impossible, the majority of the evidence comes from observational studies, but standard estimations could be biased because they ignore covariates that confound treatment decisions and outcomes. METHODS: Three observational studies were conducted to assess the benefit of Allo-SCT in hematological malignancies of multiple myeloma, follicular lymphoma and Hodgkin's disease. Two statistical analyses were performed: the propensity score (PS) matching approach and the inverse probability weighting (IPW) approach. RESULTS: Based on PS-matched samples, a survival benefit in MM patients treated by Allo-SCT, as compared to similar non-allo treated patients, was observed with an HR of death at 0.35 (95%CI: 0.14-0.88). Similar results were observed in HD, 0.23 (0.07-0.80) but not in FL, 1.28 (0.43-3.77). Estimated benefits of Allo-SCT for the original population using IPW were erased in HR for death at 0.72 (0.37-1.39) for MM patients, 0.60 (0.19-1.89) for HD patients, and 2.02 (0.88-4.66) for FL patients. CONCLUSION: Differences in estimated benefits rely on whether the underlying population to which they apply is an ideal randomized experimental population (PS) or the original population (IPW). These useful methods should be employed when assessing the effects of innovative treatment in non-randomized experiments.