The clinical outcome and its correlation with the status of minimal residual disease (MRD) was analyzed in 26 patients with chronic lymphocytic leukemia (CLL) undergoing stem cell transplantation. All patients having received autotransplant (n = 14) achieved CR which was MRD(-) in nine patients (64%) and MRD(+) in five. With a median follow-up of 26.5 months (range, 12-52), four of the five MRD(+) patients relapsed at 9, 15, 17 and 18 months after transplant, respectively. In contrast, only two patients of the nine MRD(-) patients have relapsed at 15 and 38 months (P = 0.02), and four became MRD(+) at 6, 12, 30, and 42 months after transplantation, respectively. Of the 12 patients that were allografted, three (25%) died in the early post-transplant period, one had resistant disease, and eight (67%) achieved CR. Among the latter, no evidence of MRD post-transplantation was observed in five cases, while a delayed clearance of MRD (up to 22 months after transplantation) was seen in two, and a persistent positivity of MRD after transplant was detectable in another patient until last follow-up (12 months). After a median follow-up of 43 months (range, 15-106), none of the responding patients had clinical or MRD relapse. These results show that in CLL the probability of achieving sustained MRD(-) CR is higher with allogeneic than with autologous transplants, and confirm the value of MRD assessment in the follow-up of patients transplanted for CLL.