Stem cells can be either totipotent, pluripotent, multipotent or unipotent. Totipotent cells have the capability to produce all cell types of the developing organism, including both embryonic and extraembryonic tissues. The Hematopoietic Stem Cells (HSC) are the first defined adult stem cells (ASC) that give rise to all blood cells and immune system. Use of HSCs for treatment of hematologic malignancies, which is also called bone marrow (BM) transplantation or peripheral blood stem cells (PBSC) transplantation is the pioneer of cellular therapy and translational research. However, stem cell research field is developing so fast that, innovative approaches using HSCs for treatment of refractory diseases are growing rapidly. Hematopoietic stem cell transplantation (HSCT) has been widely used to achieve cure in different hematological diseases. Applications include the treatment of marrow failure syndromes, leukemia, lymphoma, multiple myeloma (MM), certain inherited blood disorders, autoimmune diseases and as an enzyme replacement in metabolic disorders. Innovative approaches such as haploidentical stem cell transplantation, new monoclonal antibodies and immunotherapies as well as Chimeric Antigen Receptor T-cell (CAR-T cell) therapies are on the way as promising treatment options especially for patients with refractory hematologic malignancies and even in solid tumors. However, there are still some challenges remaining before some of these therapies are translated into clinical application. In this paper, HSCs including its properties, niches, clinical usage and its contribution to modern medicine today and in the future will be discussed.