The long duration of Crohn’s disease is as a rule associated with various complications that require the surgical treatment. Nutritional disorders developing in the postoperative period need to be corrected taking into consideration the totality of the mechanisms underlying their formation. Material and methods. A total of 30 patients were available for the examination based at the Moscow Clinical Research and Practical Centre during the period from 2002 to 2014. Twelve of them were women at the mean age of 60±12.9 years and 18 men aged 42±14,1 years. To optimize the nutritional support, substantiate the necessity of probiotic therapy, and develop the indications for total parenteral nutrition , the traditional treatment was supplemented by nutritional risk screening (NRS 2002) and measurement of the serum citrulline levels for diagnostics of the type and degree of intestinal failure, detection of short-chain fatty acids in coprofiltrates. Results. The following nutritional disorders were revealed in the late postoperative period: anemia in 33% of the patients, hypoproteinemia in 30%, oedema syndrome in 13%, hypokalemia in 20%, hypocalcemia in 17.0%, hyponatremia in 10%, and overweight in 6,7% of the patients. The examination of the intestine confirmed the recurrence of the disease in 16 patients (53,3%) manifested as ulcers of the mucous membrane in the area of the anastomosis. 13.3% of the patients showed the low citrulline levels in blood; all of them had undergone the subtotal resection of the small intestine in the preceding period. The metabolic activity of the intestinal microbiota evaluated from the concentration and profile of short-chain fatty acids (SCFA) in coprofiltrates exhibited the oppositely directed trends. Specifically, it was characterized by a moderate increase in the concentration of total SCFA (up to 1.5 times higher than the normal value), the selective increase in the concentrations of iso-valeric, valeric, and caproic acids, and the low content of all short-chain fatty acids in the patients who had undergone colectomy. Conclusion. The study has demonstrated that 43.3% of the patients with the complicated course of Crohn’s disease following surgical intestinal resection were in need of nutritional support. The nutritional status in 56,7% of them had to be dynamically monitored on a weekly basis. One of the reasons for the deterioration of the nutritional status was the recurrence of the disease documented in 16 patients (53,3%) as manifested in the form of ulcerative lesions of the mucous membrane in the area of the anastomosis. The special research methods employed in the study (the measurement of serum citrulline levels and short-chain fatty acid content in coprofiltrates) made it possible to elucidate the cause of nutritional disorders and to optimize the nutritional support for the patients who had undergone different types of intestinal resection for the treatment of Crohn’s disease. The comparison of the types of resection and the results of monitoring the risk of nutritional disorders with the serum citrulline levels allows for the timely diagnostics of the intestinal failure and its adequate correction in the case of incomplete adaptation of the stump.