Residual damage to marrow function has been observed in cyclophosphamide-treated or irradiated mice following recovery of marrow hematopoietic stem cells (CFU-S) and peripheral blood counts to pretreatment levels. Residual damage is evidenced by less rapid recovery of marrow CFU-S and blood counts following subsequent exposure to sublethal irradiation. Mice treated with busulfan also demonstrate residual marrow damage as evidenced by incomplete recovery of marrow CFU-S to pretreatment levels. We report here on studies to determine whether the residual marrow damage after radiation, cyclophosphamide, or busulfan therapy is exerted on the hematopoietic stroma's ability to support CFU-S proliferation (HS-P) or on the repopulating potential of the CFU-S per se. HS-P function is determined by measuring the ability of femora implanted subcutaneously into syngeneic mice to support the growth of host CFU-S. Evidence is presented to show that this function depends on fixed (nonmigrating) cells in the marrow environment. The repopulating potential of CFU-S is determined by measuring the rate of regeneration of marrow CFU-S after transplantation into lethally irradiated mice. The results of these studies indicate that exposure to 950 rad, busulfan, or cyclophosphamide all cause damage to the HS-P that persists for at least six weeks after therapy. After cyclophosphamide therapy, but not after exposure to the other two agents, HS-P function continues to improve six weeks after therapy and eventually reaches pretreatment levels. Only in busulfan-treated mice was the residual damage to the CFU-S repopulating capacity significantly more marked than damage to HS-P function.