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Losing one's immune system is a serious consequence of a stem cell transplant, putting the body at risk for viral, fungal, and bacterial infections. Rebuilding the body's immune system is a key part of the recovery.
A stem cell transplant (SCT), whether autologous or allogeneic, begins with chemotherapy, which is intended to eradicate problematic cells. Especially when administered in high doses, chemotherapy damages the bone marrow, leaving it unable to produce enough red blood cells, white blood cells, and platelets for a period of time - hence the reason for the re-infusion (or transplant) of stem cells.