The stem cell source can be either mobilized peripheral blood stem cells or bone marrow.

Autologous transplantation is commonly used for lymphomas and myeloma and less commonly for leukemia.

Autologous transplantation is also used for testicular cancer.

In patients with leukemia and lymphoma, there is considerable concern over the reinfusion of occult tumor cells along with the marrow or peripheral blood progenitors. Therefore, numerous attempts to purge tumor cells from stem cells have been undertaken. However, it is unclear whether such manipulation affects relapse, and tumor purging is not routinely performed. Arguments against purging include its cost and labor intensiveness. Moreover, for lymphoma and solid tumors, relapse occurs usually at sites of prior bulky disease, suggesting that residual tumor within the recipient, not tumor in the stem cell product, is the primary contributor to relapse. Arguments in favor of purging include gene marking studies showing that marrow involvement can contribute to relapse.

Typically fully matched donors are preferred, but various degrees of incompatibility can be tolerated with appropriate attention to prevention of rejection and graft-versus-host disease (GVHD).

Haploidentical transplantation (from family members matched at one HLA haplotype, that is, potentially as few as 6/12 loci) is considered investigational.

Conditioning regimens vary in intensity and are categorized by the duration of cytopenia and on the requirement for stem cell support. There are three levels of intensity: nonmyeloablative (NMA), reduced-intensity conditioning (RIC), and high-intensity or myeloablative conditioning (MAC).