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Thrombocytopenia has remained a major concern in post-haematopoietic stem cell transplant patients. It is a strong negative indicator for survival and is often seen in patients with advanced acute and chronic Graft versus host disease (GVHD). The pathogenesis of thrombocytopenia varies from impaired thrombopoiesis to increased turnover of platelets. The dose of CD34+ cells and that of megakaryocyte specific lineage cells (CD34+ /CD41+ and CD34+ / CD61+ ) has a positive effect on thrombopoiesis. Conditions like bone marrow fibrosis, CMV infection and ganciclovir administration affect the bone marrow environment leading to ineffective thrombopoiesis. Increased destruction of platelets is seen with GVHD, drugs, infections, thrombotic microangiopathy and platelet refractoriness due to alloimmunization. The management of thrombocytopenia includes treating the underlying conditions and supportive care with platelet transfusion. Platelet refractoriness is managed using ABO matched platelets, HLA-matched platelets or cross-matched platelets for transfusion depending on the underlying cause. Some of the recent studies have concentrated on the effect on thromobopoiesis due to maturation of megakaryocytes or ploidy and the effect of cytokines on bone marrow microenvironment. Further studies are needed to incorporate these parameters as part of routine laboratory investigation in thromobocytopenic patients along with estimation of anti-platelet antibodies for better diagnosis and management of these patients.