Background: The aim of the study was to see the influence on the outcome of Hematopoietic Stem Cell Transplantation (HSCT) with Killer Cell Immunoglobulin like Receptor (KIR) mismatching. HSCT is the main mode of treatment for different Hematological Malignancies, Solid Tumors and Autoimmune Diseases. Procedure: Around 65 patients with different Hematological Malignancies were taken from Hospital Databases who underwent Allogenic HSCT from 2012 to 2018 with median age 8yrs(1yr-15yrs). Centromeric B (Cen B) motifs donor and Non Cen B motifs (Centromeric A/A) donor were evaluated and their outcome in HSCT was considered. As for the KIR B Motifs contents, they were evaluated on the basis of greater than 2 or less than 2 and their outcome on HSCT was considered. Results: In this study we found that Cen B motifs donor had the higher survival and relapse protection for pediatric hematological malignancies (DFS 56.482, 95% confidence interval 51.763-61.201, p=0.034) (RR 0.242, 95% confidence interval 0.056-1.056, p=0.044) compared to Non Cen B motifs donor. Donor with greater than two KIR B gene motifs contents had a better survival outcome and less relapse (DFS p=0.027) (RR 0.778, 95% confidence interval 0.665-0.909, p=0.025) compared to KIR B gene motifs contents less than two. Conclusion: KIR genotyping of several best HLA-matched potentials related and unrelated donors should substantially increase the frequency of better outcome in transplants by using grafts with favorable KIR gene content, KIR mismatching between donor and recipient, selecting donor with Cen B motifs and KIR B gene motifs greater than two.