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Clostridium perfringens isolates are currently classified into one of five biotypes on the basis of the differential production of α-, β-, ε- and ι-toxins. Different biotypes are associated with different diseases of man and animals. In this study a multiple PCR assay was developed to detect the genes encoding these toxins. In addition, detection of the genes encoding the C. perfringens enterotoxin and β2-toxin allowed subtyping of the bacteria. C. perfringens isolates taken from a variety of animals, including foals, piglets or lambs, were genotyped using this assay. Most of the isolates were found to be genotype A and the gene encoding β-toxin was present in 50% of the isolates genotyped. A significant association between C. perfringens possessing the β2-toxin gene and diarrhoea in piglets was identified, suggesting that β2-toxin may play a key role in the pathogenesis of the disease.