BACKGROUND The aim of this study was to compare the concentration and immunoelectrophoretic characterization of alpha-1-antitrypsin (AAT) excreted in random fecal samples in children with acute and chronic diarrhea and in control groups. METHODS Thirty-two children with diarrhea and 23 healthy children were evaluated. The concentration and characterization of AAT were determined by radial immunodiffusion and crossed immunoelectrophoresis, respectively. RESULTS The increase in the concentration of fecal AAT was more than the upper limit for the control group (1.25 mg/g of dry stool mass) in the patients with chronic infectious diarrhea and in 52% of those with chronic non-infectious diarrhea but not in those with acute diarrhea, infectious or non-infectious. Immunoelectrophoretic analysis showed two forms of fecal AAT in both sick and healthy children. The alterations in the concentration of fecal AAT did not correlate with the immunoelectrophoretic pattern of AAT. CONCLUSIONS Our results suggest that the determination of fecal AAT could give clinically useful information about the difference between infectious and non-infectious diarrhea and the activity of characterizing disease with diarrhea.