Since changes in nutritional indices after hematopoietic stem cell transplantation (HSCT) have not been well studied, there is no definition of risk factors for the development of malnutrition, and the inception of total parenteral nutrition (TPN). We sought to analyze changes in nutritional status parameters and acute phase protein levels as qualifications for TPN. Nutritional status was assessed in 54 patients during autologous (n = 30) on allogeneic (n = 24) transplantations. Eight of 15 patients who had to be treated with TPN, needed prolonged hospitalization (>5 weeks). We assessed biochemical and anthropometric indices of nutritional status, body fat and resting energy expenditure, and acute phase protein levels on the day before starting a conditioning regimen, after chemotherapy completion, and every 7 days until engraftment, which was at least three times after stem cell infusion. Wilcoxon test and canonical analysis were used for statistical analyses. The measurement of body weight and retinol binding protein or transferrin may be useful for nutritional assessment during autologous or allogeneic HSCT, respectively. Prealbumin level, measured 8 days after the end of the conditioning regimen was helpful to make a decision about starting TPN.