Autologous bone marrow or peripheral blood stem cell transplantation are well-recognized treatments for certain malignant hematological diseases. Therapy-induced pancytopenia and immunodeficiency that lead to increased rates of bleeding complications and higher susceptibility to bacterial, viral, and fungal infections often occur following transplantation. Infections during or shortly after transplantation are more likely to be associated with the severe depression of mononuclear cells and neutrophil granulocytes, whereas post-engraftment infections in the long term are probably due to numerical and functional impairment of primarily CD4+ T-helper-cells and B-lymphocytes. A prompt and sustained engraftment of the hematopoiesis and a complete and functionally intact recovery of the immune system are necessary for a good patient outcome. The quality of reconstitution depends upon several factors, including the underlying disease, the intensity of prior therapy, and the graft source. The faster hematopoietic engraftment as well as the larger mononuclear cell inoculum transfused to recipients of blood stem cell products might be superior to bone marrow transplantation with respect to lymphohematopoietic reconstitution. In this review, data published more recently on immune reconstitution after autologous stem cell transplantation are discussed, and laboratory parameters useful for monitoring states of deficiency of cellular and humoral immunity are evaluated.