Bone marrow stem cells are the best known stem cell type and have been employed for more than 50 years, especially in pathologies of the hematopoietic and immune systems. However, their therapeutic potential is much broader, and they can also be employed to palliate neural diseases. Apart from their plastic properties, these cells lack the legal or ethical constraints of other stem cell populations, that is, embryonic stem cells. Current research addressing the integration of bone marrow–derived cells into the neural circuits of the central nervous system, their features, and applications is a hotspot in neurobiology. Nevertheless, as in other leading research lines the efficacy and possibilities of their application depend on technical procedures, which are still far from being standardized. Accordingly, for efficient research this large range of variants should be taken into account as they could lead to unexpected results. Rather than focusing on clinical aspects, this review offers a compendium of the methodologies aimed at providing a guide for researchers who are working in the field of bone marrow transplantation in the central nervous system. It seeks to be useful for both introductory and trouble-shooting purposes, and in particular for dealing with the large array of bone marrow transplantation protocols available.