Bone marrow transplantation is known to be associated with considerable morbidity and mortality. The aim of this study was to determine the influence of nutritional status and development of sick euthyroid syndrome as prognostic factors for outcome after BMT. In 100 patients who underwent transplantation the following parameters were assessed before and at day 14 and 28 after transplantation: anthropometric data (body weight, body mass index, body composition, grip strength), rapid turnover proteins transferrin and prealbumin, T4, T3, free T4, reverse T3, thyroid-stimulating hormone and thyroglobulin. Following bone marrow transplantation, 22 patients died in the short-term follow-up (group A) before day 140 after BMT, 21 patients died during further follow-up between days 140 and 365 (group B) and 57 patients survived longer than 365 days (group C). All patients experienced a significant decrease of transferrin and T3, accompanied by an increase of rT3 and rT3/T3 ratio at day 14 after BMT. At day 28 after BMT, patients in group C showed recovery from these changes with an increase of transferrin and a fall in rT3 and the rT3/T3-ratio, which was not seen in patients who died during further follow-up (groups A and B). The observed changes were independent of other prognostically relevant factors (type of disease, HLA-match, immunosuppression). Impaired nutritional status and development of a sick euthyroid syndrome, without tendency to recovery, are associated with a higher probability of fatal outcome after bone marrow transplantation and have prognostic relevance in this group of patients.