Background: HSCT related complications and disease relapse are major obstacles in successful transplantation. Addition of ATG has shown to reduce rejection and Graft Vs Host Disease (GVHD) incidence significantly. Procedure: Here we report single center retrospective analysis for relative efficacy of rabbit and equine ATG during conditioning of pediatric patients who underwent HSCT. Results: Rabbit or Equine ATG were used as a part of conditioning regimen in 117 pediatric patients. Equine ATG group was labeled as group-1 and rabbit ATG as group-2. Both groups were analyzed for transplant related complications and outcome. In thalassemia, outcomes were comparable except Group-1 had more cases of proven bacterial infection (p=0.07) and veno-occlusive disease (p=0.03). In SAA, Group-1 had early neutrophil and platelet engraftment with less number of proven bacterial infections. Acute GVHD, chronic GVHD, median chimerism at day+30 and day+90 and overall survival (OS) was comparable in two groups, both in thalassemia and SAA patients. Analysis of 7 hematological malignancy cases and 10 immunodeficiency disorders also showed similar results. Conclusion: In conclusion, effectiveness of rabbit and horse ATG were similar in thalassemia, primary immunodeficiency patients and hematological malignancy while in SAA equine ATG use was associated with early neutrophil engraftment but OS in both groups were comparable.