Patients with impaired nutritional status may show increased risk of hematopoietic stem cell transplantation (HSCT)-related complications. This study was conducted to determine whether body mass index (BMI) and other body composition parameters, such as lean body mass index (LBMI) and body fat mass (BFM), are associated with early post-transplantation toxicity and mortality in allogeneic HSCT recipients. The records of 71 patients diagnosed with acute myeloid leukemia (AML), acute lymphoblastic leukemia (ALL), chronic myeloid leukemia (CML), or myelodysplastic leukemia (MDS) who had undergone allogeneic HSCT with a conditioning regimen of busulfan-cyclophosphamide (Bu-Cy), between September 2003 and January 2009 at the Stem Cell Transplantation Unit of Gazi University Hospital were retrospectively evaluated. BMI was found to be negatively correlated with the NCI grade of mucositis, cardiotoxicity, emesis, and hyperglycemia, and with the number of erythrocyte transfusions. LBMI was also negatively correlated with the number of erythrocyte transfusions, cardiotoxicity, emesis, and hyperglycemia. BFM was negatively correlated with the day of neutrophil engraftment, and NCI grade of mucositis. Nutritional status did not have an impact on overall survival (OS), progression-free survival (PFS), or 100-day transplant related mortality (TRM).