Amino acids are an essential part of parenteral nutrition. This study aimed to determine the serum profile of amino acids and their loss in urine in patients with long-term home parenteral nutrition (HPN) during 12 h of infusion in comparison with similar parameters in the remaining 12 h as well as in healthy participants. We enrolled forty-five patients with long-term HPN for 6–75 (median, 33) months. The indication for HPN was short bowel syndrome secondary to radical resection of the small intestine following complications of Crohn’s disease. HPN was administered via two-chamber all-in-one bags prepared in a hospital pharmacy overnight for 12 h each day. The average dose of amino acids, carbohydrates and fats administered was 1·5, 3·4 and 0·68 g/kg per d, respectively, at an infusion rate of 0·11, 0·28 and 0·06 g/kg per h, respectively. The levels of essential amino acids in the serum of the patients were not significantly different from those in healthy individuals; however, of the non-essential amino acids, cystine and glutamine levels were lower and glycine and ornithine levels were higher in the patients (P < 0·05). Excretion of amino acids in the urine during 12 h of infusion at an infusion rate of 0·11 g/kg per h was 301 mg, while it was 104 mg during the remaining 12 h (P < 0·0001). Our patients on long-term HPN had a normal serum profile of essential amino acids. The total urinary excretion of amino acids during 12 h of infusion accounted for only 0·34 % (0·23–0·46) of the administered dose.