Defensins are antimicrobial peptides expressed on various epithelial surfaces. Although they are believed to contribute to intestinal homeostasis, their expression pattern in children is not well characterized. As determined by real-time polymerase chain reaction, amount of human alpha-defensins (hD)-5 and -6 mRNA in duodenal biopsies were significantly higher than in biopsies taken from the gastric mucosa. On the contrary, expression of human beta-defensins (hBD)-1 and -2 mRNA showed a significantly higher expression in the stomach. Expression of hBD3 to 6 was inconsistently detected. These results suggest a distinct role for various defensins in host defense in the upper gastrointestinal tract of children.