Total DNA was extracted and purified from luminal digesta samples (1 g) of 14-week-old (c. 43 kg bodyweight) pigs. Digoxigenin (DIG) labelled PCR products of the beta toxin gene of Clostridium perfringens type C were generated with DIG-11-UTP and chemoluminescent signals of DIG-labelled PCR products were detected on slot blots and recorded with a sensitive charge coupled densitometric camera. Detection limit and correlation of chemoluminescent signals to initial target DNA concentration were evaluated. Detection of the beta toxin gene could be achieved with 100 ag C. perfringens DNA in the presence of 1 μg unspecific DNA. The semiquantitative DIG-PCR assay was used to evaluate the relative abundance of the beta toxin gene of C. perfringens type C in purified DNA extracts from intestinal samples of pigs, which were fed a wheat/barley diet (controls), supplemented with the antibiotic avilamycin (40 mg/kg feed), a xylanase (4000 U/kg feed) or a combination of both feed additives. The antibiotic treatment significantly reduced the amount of PCR product in ileal and colon DNA extracts. Xylanase supplementation significantly reduced the amount of PCR product in colon samples, but led to an increase in jejunal samples. From the results it is concluded, that the antibiotic inhibited growth of C. perfringens type C in the ileum and colon of pigs. The semiquantitative DIG-PCR assay can be used to sensitively monitor the relative abundance of specific pathogens in the intestinal tract.