Beside diseases of the upper and lower respiratory tract acute infectious gastroenteritis is one of the most widely spread diseases during early childhood. Furthermore, the incidence of chronic inflammatory bowel diseases (CIBD) is steadily increasing. In the present study stool specimen of 220 children with infectious gastroenteritis or CIBD were analysed and compared with a group of 26 healthy patients. The diagnostic significance of granulocyte elastase levels in stool samples should be evaluated. In addition, inflammatory markers were measured in the serum and the stool specimen were subjected to a microbiological analysis. To determine the degree of inflammation the CRP, ESR, and the white-cell count were analysed. The statistical analysis of the data was carried out with the Spearman rank correlation coefficient and the Mann-Whitney U-test. Statistical significant differences of the measured PMN elastase were observed for CIBD in comparison with all other disease groups.