Hematopoietic bone marrow stem cell transplantation has been regularly used in clinical practice for over 40 years. Further research indicates that bone marrow stromal cells are also stem cells that are capable of self-renewal, proliferation and differentiation. With appropriate induction, the bone marrow stromal cells can differentiate into bone, cartilage, tendon, adipose tissue and fibrous tissue, which would potentially be applied for treating bone loss diseases. This review outlines research in understanding role of bone marrow stem cells and stem cells from other origins in bone repair, and highlight the current and potential stem cell based treatment for bone loss diseases in the future.