RATIONALE AND OBJECTIVES. The authors evaluate bone marrow signal changes on magnetic resonance (MR) imaging during high-dose chemotherapy and peripheral blood stem cell: transplantation (PBSCT). METHODS. Fourteen patients with breast cancer without bone metastases underwent four sagittal MR imaging studies with T1-weighted, T2-weighted turbo spin-echo and inversion recovery sequences with short inversion time (STIR) of the lumbar spine: (1) during initial staging, (2) prior to high-dose chemotherapy after two cycles of induction chemotherapy, (3) early after PBSCT with a leukocyte exceeding 2000/mu L, and (4) 6 to 8 weeks after PBSCT. Signal intensity ratios of averaged lumbar bone marrow to nucleus pulposus were measured and homogeneity was evaluated visually using a semiquantitative score. RESULTS. Compared with the initial finding (1): Signal intensity ratios mere altered significantly at (2): T1-weighted: -22% +/- 14, P < 0.001; T2-weighted: -11% +/- 11, P < 0.01; STIR: +33% +/- 31, P < 0.01; Signal intensity ratios were altered significantly at (3): T2-weighted: -23% +/- 12, P < 0.001, STIR: -22% +/- 23, P < 0.01; and Signal intensity ratios were altered significantly at (4): only STIR: -16% +/- 19, P < 0.01. Homogeneity scores decreased at (3) for T1-weighted and STIR sequences (-1.6 +/- 0.5 to -2.0 +/- 0.7, P < 0.01 and -1.0 +/- 0.5 to -1.4 +/- 0.5, P < 0.01, respectively) and at (4) for the fatter sequence (-1.0 +/- 0.5 versus -1.4 +/- 0.5, P < 0.01), At (4), T1-weighted images were less homogenous than initially in 3 of 14 (21%) patients. CONCLUSIONS. Magnetic resonance imaging demonstrates significant alterations of bone marrow composition during PBSCT but allows differentiation of benign therapy-related changes from those known in metastatic disease after completion of PBSCT.