Patients with hematological malignancies are well nourished prior to allogeneic hematopoietic stem cell transplantation (HSCT). HSCT and associated complications can affect body composition. The study evaluated cross-sectionally the prevalence and longitudinally the changes in lean body mass index (LBMI) in HSCT patients. Patients (n=82) were classified as normal or low LBMI. Logistic regression analyses were used to estimate odds ratios (OR) for low vs normal LBMI, between healthy volunteers and patients; for limited or extensive vs no chronic graft-versus-host-disease (GVHD); and for decreased (Karnofsky <80) vs normal functional status (>80). Patients were significantly more likely to have low LBMI at 6, 12 months, 2-3, 4-6 and >6 years than volunteers. In all, 38% of patients were below pre-HSCT LBMI at 4-6 years post-HSCT. Low LBMI was significantly associated with steroid treatment (OR 2.6, confidence intervals (CI) 1.3-5.2, P=0.008); limited (OR 5.5, CI 1.7-18.5, P=0.005) or extensive chronic GVHD (OR 20.3, CI 5.7-71.6, P<0.001); and decreased performance status (Karnofsky scores of < or =80) (OR 2.7, CI 1.3-5.9, P=0.01). Patients were more likely to have low LBMI than volunteers. Chronic GVHD and low performance status were associated with low LBMI; thus, complications and/or treatment increase the likelihood of low LBMI.