One of modern and highly effective methods of diagnostics and differential diagnostics of infected pancreonecrosis is chromatographic technique, which allows for identification of anaerobic non-clostridial infection in the foci of pancreatic destruction by the presence of volatile fatty acids, the specific end products of anaerobic bacterial metabolism. Gas chromatography (GC) - mass spectrometry (MS) also make it possible to detect in peripheral blood of patients with pancreatitis certain metabolites (di-, polyamines, and aromatic amines) that are markers of tissue (protein structure) disintegration and the degree of pancreonecrosis, which is a valuable indicator of the degree of pancreonecrosis. The presence, according to GC - MS analysis, of natural inhibitors of transamidinase (compounds of thiourea and its metabolites, the group of mercaptopurines and mercapto-derivates of imidazole) in peripheral blood at the maximum level--0.71 to 0.78 mmol/l on days 7 to 10 upon the onset of the disease--is a prognostically favorable criterion. At the same time, the presence of the maximum level of anaerobic non-clostridial infection metabolite in peripheral blood 1.12 to 1.31 mmol/l on days 7 to 10 upon the onset of the disease--is prognostically infavorable. These chromatographic criteria in combination with clinical manifestations can be considered indications to surgical treatment of infected pancreonecrosis, and the prognosis of the disease can be based on them.