Functional and morphological changes of the gastrointestinal system were assessed in patients suffering from juvenile chronic arthritis, juvenile systemic erythematosus and juvenile systemic scleroderma. The results of endoscopic investigation of the gastrointestinal tract showed inflammatory changes and cardiac and pylorus atony. Ultrasonography results suggested hepatic and pancreatic inflammatory changes, steatosis and/or amyloidosis. The above-mentioned changes were confirmed by morphological investigation (biopsy and/or autopsy). The results of the capacity tests performed in JCA (systemic form) patients revealed an impairment of liver detoxication function, and pancreas and bowel functional capacity as well. Additionally, intolerance against lactose, casein and alpha- and beta-lactoglobulin was found in most of the patients. Some symptoms of malnutrition were observed in all of them. Such factors as underlying disease severity, adverse drug effects, environmental factors (infections, nutrition) were taken into consideration as probable causes of the gastrointestinal system damage.