Citrulline is an amino acid that is not found in protein and does not enter the body through food, enteral or parenteral nutrition. It is instead synthesized exclusively by enterocytes. Therefore, citrulline concentrations in the blood can reflect the process of biosynthesis in the intestines and are directly related to changes in the function of these cells.Purpose. The aim of the study was to assess citrulline levels in children who had undergone intestinal resection during the neonatal period.Material and methods. The study included 22 children with short bowel syndrome, diagnosed by a doctor (main group; average age 3.7 months). We also included 20 children who had undergone surgery to remove less than 50% of their intestine but did not have short bowel syndrome (comparison group; average age 3 months 1 day). The control group consisted of 23 healthy children who had never had surgery on their gastrointestinal tract and did not have any congenital malformations or clinical signs of enteropathy (average age 5 months 3 days). High performance liquid chromatography-mass spectrometry (HPLC-MS) was used to measure the level of citrulline.Results. The average level of citrulline in the blood of children in the main group was 18 μmol/l (95% CI 10–22.8), in the comparison group – 17.5 μmol/l (95% CI 16–21), in the control group – 26 μmol/l (95% CI 22–3). Citrulline levels in patients who underwent surgery in the neonatal period were significantly different from those of children in the control group There were no differences in the content of citrulline between the main and comparison groups, depending on whether the colon was preserved or not and whether the ileocecal valve was present (p>0.05).Conclusion. An increase in citrulline level in the blood of children receiving therapy with a glucagon-like peptide-2 analog indicates the possibility of using this marker to monitor changes in intestinal absorption associated with physiological or pharmacological adaptation of the intestine.