Abstract Allogeneic hematopoietic stem cell transplantation (HSCT) is regarded as a curative treatment option for a variety of hematological disorders. The prognosis of allogenic (HSCT) patients is dependent on a variety of factors that affect the bone marrow microenvironment. One of these factors is the number and function of CD146+ perivascular mesenchymal cells that support the hematopoietic stem cells in the bone marrow and help their proliferation. Aim of the Study The aim of this study was to assess how the bone marrow microenvironment is being affected in patients with poor graft function post allogenic stem cell transplantation targeting the perivascular mesenchymal cells using multiparameter flow cytometric analysis of CD146 antibody. Patients and Methods Forty patients were enrolled in this study with both benign and malignant hematological diseases who underwent allogenic HSCT from matched related donors. Patients were divided into 2 equal groups: poor graft function (PGF) group and good graft function group (GGF). Patients were subjected to full history recording, clinical examination, full laboratory and radiological work-up, tissue typing and chemotherapeutic conditioning before transplantation. After transplant, bone marrow aspirate was obtained and analyzed for CD146+ perivascular mesenchymal cells using Quantitative tri-color Flow cytometric assay. Results PGF group showed significantly lower counts of WBCs, platelets and hemoglobin concentration compared to GGF group. In addition, CD34 dose showed significantly lower concentration in PGF group compared to GGF group. CD146 expression intensity on non-stem cells was significantly higher in PGF group compared to the GGF group to increase the function of these cells in supporting the proliferation of stem cells in the bone marrow. Conclusion CD146 can have a potential therapeutic role if CD146+ selected mesenchymal cells are infused in patients with refractory poor graft function to enhance the proliferation of stem cells and help in recovery of patients with PGF however further studies are warranted to document its suggested therapeutic role.