We retrospectively compared transplant outcomes for related bone marrow transplantation (rBMT), related peripheral blood stem cell transplantation (rPBSCT), unrelated bone marrow transplantation (uBMT), and unrelated cord blood transplantation (CBT) in 1,062 patients with chronic myeloid leukemia (CML) aged 20 years or over between January 1, 2000 and December 31, 2009 in Japan. The disease status was as follows: chronic phase 1 (CP1, n = 531), CP 2 or later including accelerated phase (CP2-AP, n = 342) and blastic crisis (BC, n = 189). Graft sources (GS) were rBMT (n = 205), uBMT (n = 507), rPBSCT (n = 226) or CBT (n = 124). In multivariate analysis in CP1, lower overall survival (OS) (relative risk [RR]: 6.01, 95 % confidence interval [CI]: 1.20-29.97, P = 0.029) and leukemia-free survival (LFS) (RR: 4.26, 95 % CI: 1.24-14.62, P = 0.021) were observed in uBMT compared with those in rBMT. For patients in the advanced phase of CML beyond CP1, GS had no significant impact on OS or LFS. Our results support the use of rBMT for adults with CML in CP1, but in contrast to previous reports, the superiority of rPBSCT in advanced stage of CML was not confirmed in our cohorts.