BACKGROUND To examine how killer-cell immunoglobulin-like receptor (KIR) ligand incompatibilities effect molecular relapse (MR), we compared the occurrence of bcr-abl-positive reverse-transcriptase polymerase chain reaction (RT-PCR) results in 236 CML patients (pts) after human leukocyte antigen (HLA)-identical (n=158) (group 1), HLA class I antigen mismatched and KIR-ligand compatible (n=49) (group 2), and HLA class I antigen mismatched and KIR-ligand incompatible (n=29) (group 3) hematopoietic stem-cell transplantation. METHODS We performed a retrospective single-center study. MR was evaluated using the real-time RT-PCR method for the detection of bcr-abl transcripts. RESULTS In the first group, 133 of 158 (84%) pts were in the first chronic phase of CML, and the corresponding figures were 33 of 49 (67%) pts in group 2 and 19 of 29 (64%) in group 3 (P<0.05). MR occurred in 1 of 29 (3%) pts in group 3 compared with 62 of 158 (39%) pts in group 1 and in 11 of 49 (22%) pts in group 2 (P<0.001). A hematologic relapse developed in 20 of 158 (13%) pts in group 1, 2 of 49 (4%) pts in group 2, and in 0 of 29 (0%) pts in group 3 (P<0.05). Multivariate analysis confirmed that KIR mismatches are a strong independent predictor for the occurrence of MR after transplantation (P<0.02). The 5-year overall survival rate did not vary greatly between the three groups (67% in group 1, 52% in group 2, and 66% in group 3). CONCLUSIONS These results suggest that KIR-ligand incompatibility is an important prognostic factor in the occurrence of MR after transplantation for CML.