The fecal short-chain fatty acids concentration was higher (154 +/- 46.9 mmol/L) in childhood patients than in healthy children (96.6 +/- 19.2 mmol/L). On the other hand, pH values were nonsignificantly lower in patients stool (6.78 +/- 0.75 vs. children 7.42 +/- 0.74). Using denaturing gradient gel electrophoresis specific for total bacteria, lactobacilli and bifidobacteria the microbial population was characterized in fecal samples and in duodenal biopsies. Bacteria adhering to duodenal biopsies were not dominating in stool samples. More than 50 % of detected bacterial species belonged to as yet uncultured strains.