Hematopoietic stem cell transplantation (HSCT) has been used as a treatment modality in patients with chronic lymphocytic leukemia (CLL). Allogeneic HSCT is the only therapy at present that has curative potential in patients with CLL. Allogeneic HSCT using standard myeloablative regimens has been generally associated with high treatment mortality rates and autologous HSCT with high relapse rates. Over the last decade the use of reduced intensity conditioning (non-myeloablative) regimens have reduced the treatment-related mortality after allogeneic-HSCT without affecting the graft-versus-leukemia effectiveness. In addition, the development of molecular and biologic markers has identified high-risk CLL patients that may benefit from earlier treatment with HSCT. This review summarizes the use of existing prognostic markers in CLL and their use in HSCT, and the advances, indications and clinical outcomes of both autologous HSCT and allogeneic HSCT.